title: d80 WT, proximal lung, sample 3

description:
Library name: AXH064
10x Genomics


title: d80 WT, proximal lung, sample 2

status: Public on Jun 18 2025

type: SRA

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

country: USA

institute: Case Western Reserve University

description:
Library name: AXH063
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.1.0
Assembly: Oar_v4.0/oviAri4 (Texel)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Ovis aries

source_name: Proximal lung

extract_protocol:
i. For single cell isolation from proximal or distal lung ~300 mg of tissue was cut into 2-3 mm pieces and subjected to two rounds of digestion.  First in 5ml of collagenase solution (200 U/ml collagenase, 40 IU/ml DNase I  (all from Worthington), 3 mM CaCl2, at 37°C, with continuous stirring for 30-40 min. Alternatively, Roche Liberase TL (Millipore Sigma) containing 100 µg/ml collagenase was used.  Tissue clumps were then disassociated by pipetting 10 times in a 5 ml serological pipette and left to settle for 3-4 min at which point the supernatant was collected and stored on ice as cell suspension 1. Second, 5 ml of fresh collagenase digestion solution as above was added to the settled tissue clumps remaining after the first digestion and again stirred at 37°C for 30-40 min, at which point very little tissue debris remained. The supernatant (cell suspension 2) was pooled with cell suspension 1 and together passed through a cell strainer (200 µm, pluriSelect) to remove any tissue debris. The strained cell suspension was then centrifuged at 300 x g for 5 min, washed once in HBSS (Sigma Aldrich) + 2% FBS and centrifuged again. 4 ml of 1× Red Blood Cell Lysis Solution (Miltenyi Biotec 130-094-183) was added to the cell pellet which was vortexed for 5 seconds and then incubated for 5 minutes at room temperature. After 10 ml of HBSS with 2% FBS was added, the mixture was centrifuged at 300 × g for 5 min and the supernatant was removed. The cell pellet was then digested with 3 ml of Accutase (Stem Cell Technologies, #AT104) for 15-25 min with frequent gentle pipetting with a wide-bore pipette after which time cells were visualized under a microscope. If any cell clumps persisted these were collected by centrifugation and further digested with 3 ml of Accutase for an additional 10-15 min. Accutase was removed by washing the cells with 5 ml HBSS + 2% FBS, followed by centrifugation to collect the cells. The supernatant was discarded, and the cell pellet was resuspended in 0.5-1.0 ml HBSS, passed through a 20-µm mini cell strainer (pluriSelect) and cells counted. ii) Single-cell RNA-sequencing and analysis ii) Approximately 3000- 5000 cells per tissue sample were used for scRNA-seq using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3, or v3.1.  After quality control of both cDNA and final libraries using Tapestation, the libraries were sequenced on a NovaSeq 6000 machine. Reads were aligned to the Oar_v4.0/oviAri4 (Texel) genome using Cell Ranger 3.1.0. Cells were filtered for quality using cuts for standard metrics: library size, number of detected genes and mitochondrial read percentage. Ribosomal protein genes were also filtered out. The resulting objects were normalized and batch-corrected using the Seurat R package, version 5.1.0, followed by clustering and UMAP (Uniform Manifold Approximation and Projection) dimensionality reduction. Seurat was also used to find cluster markers by performing differential gene expression analysis between clusters using the receiver operating characteristic (ROC) method.
Libraries generated from single cells according to the manufacturer's protocol for 10X Genomics Chromium Single Cell 3' Reagent Kits v3 or 3.1.

tag: tissue

value: Proximal lung

tag: Sex

value: male

tag: disease state

value: WT


title: d80 CF, distal lung, sample 4

description:
Library name: AXH118
10x Genomics

source_name: Distal lung

value: Distal lung

value: CF


title: d80 CF, distal lung, sample 2

description:
Library name: AXH081
10x Genomics


title: Library_MH4_iPCR_bc_fragment_mapping

status: Public on Jul 01 2025

city: Amsterdam

first: Noud

last: Klaassen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Insitute

description: Library name: PARM_Training_Library_v2_MH4_barcode_fragment_mapping

library_source: other

data_processing:
See methods
Assembly: hg19
Supplementary files format and content: count tables and normalized (log2RPM) data

molecule: other

organism: Homo sapiens

source_name: plasmid

growth_protocol: cells were cultured according to manufacters protocol

extract_protocol:
Standard RNA extraction protocols see methods paper
Various different protocols

treatment_protocol: cells were transfected by either nucleofection or lipofection

tag: cell line

value: plasmid


title: d80 CF, distal lung, sample 3

description:
Library name: AXH117
10x Genomics


title: d80 WT, distal lung, sample 4

description:
Library name: AXH062
10x Genomics


title: d80 WT, distal lung, sample 3

description:
Library name: AXH061
10x Genomics


title: d80 WT, distal lung, sample 1

description:
Library name: AXH034
10x Genomics


title: Day 120 natural CF, proximal lung, sample 2

description: 10x Genomics

value: Female


title: d80 WT, distal lung, sample 2

description:
Library name: AXH060
10x Genomics


title: Day 120 cloned CF, proximal lung, sample 3

description: 10x Genomics

value: Male


title: Day 120 cloned CF, proximal lung, sample 1

description: 10x Genomics


title: Day 120 natural CF, proximal lung, sample 1

description: 10x Genomics


title: Day 120 cloned CF, proximal lung, sample 4

description: 10x Genomics


title: Day 120 cloned CF, proximal lung, sample 2

description: 10x Genomics


title: Day 120 WT, proximal lung, sample 2

description: 10x Genomics


title: Day 120 WT, proximal lung, sample 3

description: 10x Genomics


title: Day 120 WT, proximal lung, sample 1

description: 10x Genomics


title: Day 120 natural CF, distal lung, sample 2

description: 10x Genomics


title: Day 120 cloned CF, distal lung, sample 4

description: 10x Genomics


title: d80 WT, proximal lung, sample 1

description:
Library name: AXH035
10x Genomics


title: Day 120 cloned CF, distal lung, sample 5

description: 10x Genomics


title: Day 120 cloned CF, distal lung, sample 3

description: 10x Genomics


title: Day 120 cloned CF, distal lung, sample 2

description: 10x Genomics


title: Day 120 WT, proximal lung, sample 4

description: 10x Genomics


title: Day 120 cloned CF, distal lung, sample 1

description: 10x Genomics


title: Day 120 natural CF, distal lung, sample 1

description: 10x Genomics


title: Day 120 WT, distal lung, sample 4

description: 10x Genomics


title: Term cloned CF 9 hr, proximal lung, sample 2

description: 10x Genomics


title: d80 CF, distal lung, sample 1

description:
Library name: AXH057
10x Genomics


title: Day 120 WT, distal lung, sample 1

description: 10x Genomics


title: Term natural CF 16 hr, proximal lung

description: 10x Genomics


title: Term cloned CF 9 hr, proximal lung, sample 1

description: 10x Genomics


title: Day 120 WT, distal lung, sample 2

description: 10x Genomics


title: Term CF (nat exon 2) 18 hr, proximal lung

description: 10x Genomics


title: Term WT 5.5 hr, proximal lung

description: 10x Genomics


title: Term WT 62 hr, proximal lung

description: 10x Genomics


title: Term WT 3d (~72 hrs), proximal lung

description: 10x Genomics


title: Term natural CF 60 hr, proximal lung

description: 10x Genomics


title: Term WT 6 hr, proximal lung

description: 10x Genomics


title: Term cloned CF 9 hr, distal lung, sample 2

description: 10x Genomics


title: Term cloned CF 9 hr, distal lung, sample 1

description: 10x Genomics


title: Term natural CF 60 hr, distal lung

description: 10x Genomics


title: Term WT 62 hr, distal lung

description: 10x Genomics


title: Term CF (nat exon 2) 16 hr, distal lung, sample 2

description: 10x Genomics


title: Term WT 5.5 hr, distal lung

description: 10x Genomics


title: Term CF (nat exon 2) 16 hr, distal lung, sample 1

description: 10x Genomics


title: Term WT 14-18 hr, distal lung

description: 10x Genomics


title: Day 120 WT, distal lung, sample 3

description: 10x Genomics


title: Term WT 14 hr, distal lung

description: 10x Genomics


title: Term natural CF 16 hr, distal lung

description: 10x Genomics


title: Term WT 3d (~72 hrs), distal lung

description: 10x Genomics


title: Term WT 6 hr, distal lung

description: 10x Genomics


title: 22d+dasatinib_3

status: Public on Jun 05 2025

city: Beijing

first: Ke

last: Li

address: 1 Tian Tan Xi Li

department: Institute of Medicinal Biotechnology

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Sample 9

library_source: transcriptomic

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

source_name: Bone marrow

extract_protocol:
cells were collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: SupB15 cells

tag: cell type

value: B lymphoblast

tag: genotype

value: BCR-ABL

tag: treatment


title: 22d+dasatinib_2

description: Library name: Sample 8


title: Dasatinib_3

description: Library name: Sample 6

value: Dasatinib


title: Dasatinib_1

description: Library name: Sample 4


title: Control_3

description: Library name: Sample 3

value: Control


title: 22d+dasatinib_1

description: Library name: Sample 7


title: Term WT 14 hr, proximal lung

description: 10x Genomics


title: Control_1

description: Library name: Sample 1


title: HD-3

status: Public on May 18 2025

city: Bethesda

first: Jyothi

last: Padiadpu

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: 10x Genomics

data_processing:
Demultiplexing, barcoding, and gene counting was done with Cell Ranger version 7.2.0
Normalization, scaling, dimensionality reduction, integration and differential expression analysis was done in Seurat version 5.0.1
Doublets were identified with scDblFinder version 1.16 and celltype annotations were identified using Azimuth version 0.4.6
Pathway analysis was performed using Qiagen Ingenuity Pathway Analysis software version 107193442
Assembly: hg38
Supplementary files format and content: R data object of Seurat integrated samples
Supplementary files format and content: Filtered H5 feature barcode matrix files from Cellranger Count

source_name: blood

extract_protocol:
Purified CD4+ T cells from frozen PBMCs of healthy donors and acute ATL patients were stimulated briefly with 2 mg/ml plate-bound anti-CD3 and 1 mg/ml soluble anti-CD28 in the presence of 500 IU/ml recombinant human IL-2 for 4 hours at 37°C. Cells were harvested and loaded into separate channels of a Single Cell Chip G with reverse transcriptase reagent mixture and 5’gel beads according to the manufacturer’s protocol (10X Genomics; Pleasanton, CA)
Chips were next loaded into the 10X Genomics Chromium Controller for single-cell partitioning, immediately followed by emulsion recovery from the chip and incubated in a MJ Research PTC-200 Thermal Cycler for the reverse transcription reaction, cDNA isolation and library preparation were completed per the manufacturer’s protocol. Isolated cDNA was amplified (11 cycles) and was used for the preparation of a gene expression library with the Chromium Next GEM Single Cell 3’ Reagent kits v3.1 (10X Genomics). The quality of the cDNA and library was evaluated using the D1000 high-sensitivity kits on a 2200 TapeStation system (Agilent; Santa Clara, CA)

value: blood

value: PBMC

value: healthy donor


title: HD-1

description: 10x Genomics


title: HD-2

description: 10x Genomics


title: Day 120 cloned CF, proximal lung, sample 5

description: 10x Genomics

value: Proximal lung


title: ATL-5

description: 10x Genomics

value: adult T-cell leukemia


title: ATL-3

description: 10x Genomics


title: ATL-2

description: 10x Genomics


title: ATL-1

description: 10x Genomics


title: Prdm1 KO 24h IL-2 Rep2

status: Public on May 16 2025

data_processing:
RNA-seq data was processed using the RNA-seek workflow v1.8.0 (https://doi.org/10.5281/zenodo.5223025) and the NIH HPC Biowulf cluster. (http://hpc.nih.gov). In brief, reads were trimmed using cutadapt v1.1872 and aligned to the mm10 reference genome and GENCODE release M21 using STAR v2.7.6a73 in 2-pass basic mode. Expression levels were quantified with RSEM v1.3.074.
Assembly: mm10
Supplementary files format and content: NHLBI-99.RSEM_genes_expected_counts.tsv: raw counts table
Supplementary files format and content: NHLBI-99.RSEM.genes.FPKM.all_samples.txt: FPKM-normalized counts table

organism: Mus musculus

source_name: Splenic Treg

extract_protocol:
Cells were harvested and total RNA was extracted using Direct-zol RNA MiniPrep kit (#R2052, Zymo Research) according to the kit’s protocol.
100 ng of total RNA was used to prepare RNA-Seq libraries using the KAPA RNA HyperPrep Kit (#KK8542, KAPABIOSYSTEMS) per the manufacturer’s protocol.

value: Splenic Treg

value: Prdm1-CKO (Prdm1fl/flFoxp3YFP-cre)


title: Prdm1 KO 24h IL-2 Rep1


title: WT 24h IL-2 Rep1

value: WT (Foxp3YFP-cre)


title: WT 24h IL-2 Rep2


title: SF_2

status: Public on Apr 14 2025

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: Sample 2

data_processing:
Fastq files were generated using 10X Cell Ranger (version 7.0). Starting with raw Illumina BCL files from the sequencing output, the cellranger mkfastq command with default parameters was used to generate fastq files.
Fastq files were aligned using 10X Cell Ranger (version 7.0). The cellranger count command with default parameters was used to align the expression reads to the GRCh38 build of the human transcriptome (refdata-gex-GRCh38-2020-A) and generate a gene expression count matrix.
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: *_barcodes.tsv.gz, *_features.tsv.gz, *_matrix.mtx.gz for all samples. Filtered counts of sequencing reads

extract_protocol:
Nuclei isolation was completed using the 10x Chromium Nuclei Isolation Kit (PN-1000494, 10x Genomics)
RNA libraries were prepared using the 10x Genomics Chromium Nuclei Isolation Kit Protocol for Single Cell 3’ Gene Expression (RevA)

treatment_protocol: hCO were matured using the SF or DM protocol. At the conclusion of the experiment, media was aspirated and hCO were washed with ice cold PBS-. Intact hCO were pooled with up to 70 hCO per sample (n = 2 per maturation protocol). All PBS- was removed and hCO were snap frozen in liquid nitrogen and stored at -80oC.


title: BMT-CTN-460_PCON_CD3

status: Public on Mar 20 2025

city: Boston

first: Leslie

last: Kean

state: MA

address: 300 Longwood Ave

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: BMT-CTN-460_PCON_CD3

data_processing:
Analysis of the 5’ scRNA + TCR data was performed as follows: FASTQ files were aligned with Cell Ranger v7.1.0 using GRCh38 as the reference genome, then imported into Python v3.10.12. Droplets were filtered for protein-coding, TR_C_, and IG_C_ genes per annotations from Ensembl v112. We then performed QC to analyze only cells with a mitochondrial gene expression of less than 10%, between 700 and 6,000 unique genes, and between 1,000 and 25,000 transcripts. We further filtered the genes to those expressed in at least 10 cells and then selected the 7,500 most variable genes (running Scanpy v1.10.2) plus PTPRC and CD3E. To filter for T cells, we performed initial clustering with Scanpy and removed clusters with low CD3E expression. We then performed clustering using an encoding generated with scvitools v1.1.5 and removed another 2 clusters low in CD3E expression. For all downstream analyses, we focused on D28 and D365 samples. We manually annotated separate D28 and D365 CD4 and CD8 clusters using a list of T cell marker genes and studying the list of differentially expressed genes within each cluster after batch correcting by patient. For TCR analysis, we extracted clonotype groupings generated by Cell Ranger, which were subsequently aligned with Adaptive TRB CDR3 sequences when appropriate.
Supplementary files format and content: .h5 matrix of single-cell RNA-seq
Supplementary files format and content: .csv file of clonotype information for single-cell TCR-seq

source_name: Blood

extract_protocol:
After transplant infusion, empty stem cell graft bags or syringes were obtained and shipped to a central reference laboratory for graft cell isolation. Peripheral blood samples were shipped by each site to the central BMT CTN Repository operated by the NMDP where peripheral blood mononuclear cells, whole blood, and plasma were isolated and frozen in separate aliquots from each timepoint. A subset of the PBMCs from patients analyzed by flow cytometry who had PBMCs frozen from the leftover graft bag/syringe underwent scRNA- and TCR-Seq. These PBMCs were enriched for CD3+ T cells through MACS using the Miltenyi human Pan T cell Isolation Kit (Miltenyi Biotec) before sequencing.
Approximately 16,500 cells per sample were loaded onto a 10X Chromium Instrument (10x Genomics) according to manufacturer’s instructions. GEX libraries were generated using Chromium Next GEM Chip K Single Cell Kit v2 (10X Genomics) and normalized to 12nM; VDJ libraries were generated using Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics) and normalized to 3nM. Pooled GEX and VDJ libraries were sequenced on Illumina NovaSeq S4 at the Broad Institute.

value: Blood

value: CD3+ T cell


title: LCL transformed under 21% O2 by EBV, replicate 1, H3K27ac, ChIP

status: Public on May 07 2025

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

description:
Library name: 21__O2_LCL_H3K27ac_rep1
H3K27ac ChIP

library_source: genomic

data_processing:
For RNA-seq, adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR2.5.2b 85. Feature Counts was used to estimate the number of reads mapped to each contig 86. Only transcripts with at least 5 cumulative mapping counts were used in this analysis. DESeq2 was used to evaluate differential expression (DE) 87. DESeq2 uses a negative binomial distribution to account for overdispersion in transcriptome datasets. It uses a conservative analysis that relies on a heuristic approach. Each DE analysis used pairwise comparison between the experimental and control groups. Differentially expressed genes were identified and a P-values < 0.05 and absolute fold change > 2 cutoff was used. Differentially expressed genes (DEGs) were subjected to Enrichr analysis which was employed to perform gene list-based gene set enrichment analysis on the selected gene subset. The algorithm used to calculate combined scores was described previously 88. P value and log2 fold change were generated with DESeq2 under default settings with Wald test and normal shrinkage, respectively.
For ChIP-seq, read quality was assessed using FastQC to ensure no biases such as GC skew or PCR artifacts. ChIP-seq reads were aligned to the human genome (hg19) using default settings using Bowtie2, except -k was set to 1, with a mappability rate of 94–98%. Peaks were called using MACS v2.1.074 with an FDR threshold of ≤ 0.99(Ref), followed by IDR analysis (v2.0.3) with an IDR threshold of ≤ 0.02, as recommended by the ENCODE consortium to ensure peak reproducibility. Peaks in blacklist regions were excluded from downstream analysis. Bigwig files were generated using deepTools v3.5.6.
Assembly: hg19
Supplementary files format and content: For RNA-seq, tab-delimited text files include Log2FoldChange value (21%_O2_LCL v.s. 1%_O2_LCL), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

molecule: genomic DNA

source_name: B lymphocytes

growth_protocol: Purified naïve B cells were incubated with B95-8 EBV at a multiply of infection (MOI) of 0.1 for 1 hour at 37°C in a 5% CO₂ incubator to facilitate viral entry. Following infection, cells were washed with serum free RPMI-1640 medium and resuspended in complete culture medium (RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin). To assess the impact of oxygen levels on EBV transformation, infected B cells were cultured under two distinct oxygen conditions: 1) normoxia (21% O₂): cells were maintained in a standard tissue culture incubator (ThermoFisher) at 37°C with 5% CO₂; 2) hypoxia (1% O₂): cells were placed in a hypoxia incubator (ThermoFisher) set to 1% O₂, 5% CO₂, and 94% N₂ at 37°C. Cells were cultured for 28 days, during which they proliferated and transformed into lymphoblastoid cell lines (LCLs). LCLs were passaged every 3–4 days by replacing 2/3 of the medium with fresh RPMI-1640 supplemented with 10% FBS to support cell growth.

extract_protocol:
For RNA extraction, total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination. For chromatin samples, sample was prepared using the iDeal ChIP-seq kit for Histones (C01010059, HILOGIC Diagenode) following the sonication using Diagenode Pico.
For RNA-seq library preparation, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA). For ChIP-seq libaray preparaion, DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S, NEB) and sequenced at the Tufts Genomics Core.

treatment_protocol: Primary B cells were transformed by EBV under 21% O2 or 1% O2 tension.

value: B lymphocytes

value: EBV transformed LCL

value: 21% Oxygen


title: BMT-CTN-460_Bag_CD3

description: Library name: BMT-CTN-460_Bag_CD3


title: BMT-CTN-460_DONOR_CD3

description: Library name: BMT-CTN-460_DONOR_CD3


title: Dasatinib_2

description: Library name: Sample 5

value: Bone marrow

value: SupB15 cells

value: B lymphoblast


title: Control_2

description: Library name: Sample 2

value: BCR-ABL

value: Control


title: BMT-CTN-460_Day_365_CD3

description: Library name: BMT-CTN-460_Day_365_CD3


title: LNCaP, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_LNCaP_Replicate2

source_name: LNCaP

value: LNCaP

value: Prostate carcinoma


title: BMT-CTN-435_Bag_CD3

description: Library name: BMT-CTN-435_Bag_CD3


title: BMT-CTN-423_Day_365_CD3

description: Library name: BMT-CTN-423_Day_365_CD3


title: BMT-CTN-435_Day_28_CD3

description: Library name: BMT-CTN-435_Day_28_CD3


title: BMT-CTN-435_Day_365_CD3

description: Library name: BMT-CTN-435_Day_365_CD3


title: ATL-4

description: 10x Genomics

value: blood

value: PBMC


title: BMT-CTN-423_PCON_CD3

description: Library name: BMT-CTN-423_PCON_CD3


title: BMT-CTN-405_PCON_CD3

description: Library name: BMT-CTN-405_PCON_CD3


title: BMT-CTN-423_Bag_CD3

description: Library name: BMT-CTN-423_Bag_CD3


title: BMT-CTN-405_Day_28_CD3

description: Library name: BMT-CTN-405_Day_28_CD3


title: BMT-CTN-423_Day_28_CD3

description: Library name: BMT-CTN-423_Day_28_CD3


title: BMT-CTN-393_Day_365_CD3

description: Library name: BMT-CTN-393_Day_365_CD3


title: BMT-CTN-405_Bag_CD3

description: Library name: BMT-CTN-405_Bag_CD3


title: SF_1

description: Library name: Sample 1


title: BMT-CTN-393_PCON_CD3

description: Library name: BMT-CTN-393_PCON_CD3


title: BMT-CTN-393_Day_28_CD3

description: Library name: BMT-CTN-393_Day_28_CD3


title: BMT-CTN-393_Bag_CD3

description: Library name: BMT-CTN-393_Bag_CD3


title: BMT-CTN-435_PCON_CD3

description: Library name: BMT-CTN-435_PCON_CD3


title: BMT-CTN-336_BAG_CD3

description: Library name: BMT-CTN-336_BAG_CD3


title: BMT-CTN-336_28_CD3

description: Library name: BMT-CTN-336_28_CD3


title: BMT-CTN-292_DONOR_CD3

description: Library name: BMT-CTN-292_DONOR_CD3


title: BMT-CTN-292_Day_365_CD3

description: Library name: BMT-CTN-292_Day_365_CD3


title: BMT-CTN-336_365_CD3

description: Library name: BMT-CTN-336_365_CD3


title: BMT-CTN-299_PCON_CD3

description: Library name: BMT-CTN-299_PCON_CD3


title: BMT-CTN-292_Day_28_CD3

description: Library name: BMT-CTN-292_Day_28_CD3


title: BMT-CTN-292_Bag_CD3

description: Library name: BMT-CTN-292_Bag_CD3


title: BMT-CTN-405_Day_365_CD3

description: Library name: BMT-CTN-405_Day_365_CD3


title: BMT-CTN-252_Day_365_CD3

description: Library name: BMT-CTN-252_Day_365_CD3


title: BMT-CTN-252_PCON_CD3

description: Library name: BMT-CTN-252_PCON_CD3


title: BMT-CTN-299_Day_28_CD3

description: Library name: BMT-CTN-299_Day_28_CD3


title: BMT-CTN-252_Day_28_CD3

description: Library name: BMT-CTN-252_Day_28_CD3


title: BMT-CTN-231_365_CD3

description: Library name: BMT-CTN-231_365_CD3


title: BMT-CTN-231_BAG_CD3

description: Library name: BMT-CTN-231_BAG_CD3


title: BMT-CTN-231_PCON_CD3

description: Library name: BMT-CTN-231_PCON_CD3


title: BMT-CTN-252_DONOR_CD3

description: Library name: BMT-CTN-252_DONOR_CD3


title: BMT-CTN-185_BAG_CD3

description: Library name: BMT-CTN-185_BAG_CD3


title: BMT-CTN-336_PCON_CD3

description: Library name: BMT-CTN-336_PCON_CD3


title: BMT-CTN-185_365_CD3

description: Library name: BMT-CTN-185_365_CD3


title: BMT-CTN-185_28_CD3

description: Library name: BMT-CTN-185_28_CD3


title: BMT-CTN-179_Day_28_CD3

description: Library name: BMT-CTN-179_Day_28_CD3


title: BMT-CTN-179_PCON_CD3

description: Library name: BMT-CTN-179_PCON_CD3


title: BMT-CTN-179_Day_365_CD3

description: Library name: BMT-CTN-179_Day_365_CD3


title: BMT-CTN-021_PCON_CD3

description: Library name: BMT-CTN-021_PCON_CD3


title: BMT-CTN-292_PCON_CD3

description: Library name: BMT-CTN-292_PCON_CD3


title: BMT-CTN-021_Day_365_CD3

description: Library name: BMT-CTN-021_Day_365_CD3


title: BMT-CTN-021_Bag_CD3

description: Library name: BMT-CTN-021_Bag_CD3


title: BMT-CTN-021_Day_28_CD3

description: Library name: BMT-CTN-021_Day_28_CD3


title: RNA-seq, K562, Donor + B2M RNP, IST

status: Public on Feb 25 2025

city: La Jolla

first: Graham

last: McVicker

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: Library name: RNA_06

data_processing:
RNA-seq analysis
Raw reads were demultiplexed and trimmed using Cutadapt.
Trimmed reads were aligned to human reference genome hg38 using BWA-MEM.
Aligned reads were post-processed with Samtools and counted with Featurecounts.
Superb-seq analysis
Raw reads were processed into annotated alignments to hg38 using Split-pipe (v1.1.1).
Alignments were processed into count matrices of Cas9 edits and genes using Sheriff.
Assembly: hg38
Supplementary files format and content: TSV files of Cas9 edit counts, gene counts, and metadata.

growth_protocol: All cells were grown in RPMI-1640 with 10% heat-inactivated fetal bovine serum and penicillin/streptomycin, 37C, 5% CO2.

extract_protocol:
For RNA-seq, T7 RNA was extracted from IST reactions by TRIzol LS and column purification. For Superb-seq, combinatorially barcoded cDNA was generated by Evercode WT Mini kit (Parse Biosciences) and extracted from fixed cells by SPRI beads according to Evercode kit instructions.
RNA-seq library was prepared by QIAseq UPXome kit (QIAGEN). Single-cell Superb-seq library was prepared by Evercode WT Mini kit (Parse Biosciences). Both libraries were prepared according to kit instructions.

treatment_protocol: Jurkat or K562 cells were edited with Superb-seq donor DNA and/or Cas9-guide RNA ribonucleoprotein (RNP) by electroporation. For bulk RNA-seq, cells were edited at CTLA4 or B2M, and T7 in situ transcription (IST) was performed on fresh nuclei isolated by the Omni-ATAC protocol. For single-cell Superb-seq, pools of unedited K562 cells, ARID1A- and/or SMARCA4-edited cells, and CHD4- or CHD3/CHD4-edited cells were paraformaldehyde fixed with an off-the-shelf kit (Parse Biosciences), and IST was performed on fixed cell pools.

value: Donor + B2M RNP, IST


title: Superb-seq, K562, BAF NuRD complexes, 10k cells

description: Library name: SCRNA_02

data_processing:
Split-pipe was used to pre-process, align, and annotate reads using default settings. Input FASTQ files, output BAM file.
Sheriff was used to process aligned reads into edit and gene counts. Input BAM file, output count matrices and summary tables.
Assembly: hg38
Supplementary files format and content: Tab-separated text files of edit counts, gene counts, and metadata

growth_protocol: Suspension cells (K562) were grown in RPMI-1640. Adherent cells (293FT, U2OS) were grown in DMEM, dissociated with TrypLE. All cell cultures were supplemented with 10% heat-inactivated FBS and penicillin/streptomycin, and incubated at 37°C, 5% CO2.

extract_protocol:
After in situ transcription, cells were immediately washed and processed into scRNA-seq cDNA by Evercode WT Mini v2 or v3 kit (Parse Biosciences). Barcoded cDNA was extracted from fixed cells by SPRI beads according to kit instructions.
Superb-seq libraries were prepared by Evercode WT Mini v2 or v3 kit (Parse Biosciences).

treatment_protocol: Cells were edited by electroporation with Cas9-guide ribonucleoprotein (RNP) and Superb-seq T7 promoter. Pools of unedited (electroporation only) or edited cells were fixed by Evercode Cell Fixation kit (Parse Biosciences) and subjected to overnight in situ transcription.

value: Pooled + IST


title: Superb-seq, K562, BAF NuRD complexes, 500 cells

description: Library name: SCRNA_01


title: RNA-seq, K562, B2M RNP, IST

description: Library name: RNA_05

value: B2M RNP, IST


title: BMT-CTN-231_28_CD3

description: Library name: BMT-CTN-231_28_CD3

value: Blood


title: RNA-seq, Jurkat, Donor + CTLA4 RNP, IST

description: Library name: RNA_03

source_name: Jurkat E6-1

value: Jurkat E6-1

value: Donor + CTLA4 RNP, IST


title: BMT-CTN-185_PCON_CD3

description: Library name: BMT-CTN-185_PCON_CD3

value: CD3+ T cell


title: RNA-seq, Jurkat, CTLA4 RNP, Mock

description: Library name: RNA_01

value: CTLA4 RNP, Mock


title: RNA-seq, Jurkat, CTLA4 RNP, IST

description: Library name: RNA_02

value: CTLA4 RNP, IST


title: G7883_resistant_H226_cells_rep2 (Micro-Capture C)

status: Public on Feb 12 2025

city: South San Francisco

first: Bence

last: Daniel

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

description: Library name: Resistant_G7883_rep2

data_processing:
Adaptor sequences were trimmed from FASTQ files using TrimGalore (v0.6.10, Babraham Institute)
Reads were aligned to the reference genome hg38 using BWA mem (v0.7.18), and the resulting files were parsed to identify junction contacts using pairtools parse2 (v1.1.0).
Reads were sorted and deduplicated using pairtools sort and pairtools dedup, and converted to BED files using a custom Python script. Promoter-linked junction pairs were identified by intersecting the BED files with a reference file containing genomic regions of interest, and the results were filtered and split into different viewpoints.
Assembly: hg38
Supplementary files format and content: Normalized (CPM) bigwig files that contain gene promoter-linked (promoter-aligning) sequencing reads of all investigated promoters.

source_name: Lung

growth_protocol: Cell lines used in this study were obtained from American Type Culture Collection (ATCC). Cells were maintained in RPMI 1640 supplemented with 10% FBS (Sigma-Aldrich Corporation), 2 mM L-glutamine (Gibco Life Sciences) and Penicillin-Streptomycin in a humidified incubator maintained at 37°C with 5% CO2.

extract_protocol:
Cells were scraped and crosslinked in the presence of 1% formaldehyde (in PBS) for 10-minutes in suspension followed by the addition of 1.5ml 1M Glycine and further incubation for 5-minutes at room temperature. Cells were washed in ice-cold PBS, counted, and 3-4x106 cell aliquots were prepared for nuclei isolation with the following MCC lysis buffer: 10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin and 1% BSA in nuclease-free H2O. Each cell aliquot of 3x106 was resuspended in 500ul MCC lysis buffer and incubated on ice for 5-minutes. Cells were spun down, washed in ice-cold PBS, and washed in nuclease-free H2O before proceeding to MNase digestion with 90-130U of MNase for 3x106 cells that went on for 1-hour at 37C while shaking in a thermomixer (Eppendorf) at 550rcf. MNase was stopped by the addition of EGTA. At this point, nuclei were split into two tubes, and end-repair and proximity ligation were performed overnight. On the next day, nuclei were spun and subjected to proteinase K digestion at 65C overnight. DNA was column purified (Minelute, Qiagen) and eluted in 130ul H2O for sonication with Covaris E220 model using the following settings: Fill Level – 10, Duty Cycle – 15, PIP – 300, Cycles/Bursts – 200; sonicated for 5-minutes. DNA was cleaned up with Minelute, quantified and subjected to library preparation with Ovation Ultralow V2 Library Systems (Tecan) using 100ng DNA and 8 PCR cycles. Amplified libraries were subjected to hybridization with biotinylated oligonucleotide pools that were designed by the HyperDesign Team (Roche) and synthesized by Roche. All hybridization reagents were purchased from Roche as part of the KAPA Hyper Prep kit, and hybridization, pull-down, and washes were performed per manufacturer’s instructions. Bead-bound libraries were amplified with the PCR reagents from the Ovation Ultralow Library V2 Kit (Tecan). Libraries were quantified and sequenced on a NovaSeq 6000 with 2x150bp configuration. MCC analysis was performed on two biological replicates per condition, and each biological sample was defined as a pooled total of 3 different MNase conditions (90U, 110U and 130U, 3x106 cells per MNase reaction), each split into two ligation reactions for subsequent downstream steps as described above.
OTHER: Micro-Capture C (MCC)

treatment_protocol: TEAD small molecule inhibitor (SMI) resistant NF2 null NCI-H226 were generated by incubation with increasing concentrations of TEAD SMI over time (0.25 μM to 3 μM at bi-weekly with 0.1-0.5 μM increments), ensuring at least a 25% confluence at all times. The generation of the resistant cell lines was done using pooled populations of survivor cells. Resistant cells were grown in the presence of 5 μM GNE-7883. NCI-H226 cells treated with 2.5 μM GNE-7883 for 48-hours were collected for acute treatment conditions.

value: Lung

value: Mesothelioma

value: wild type


title: RNA-seq, K562, Donor + B2M RNP, Mock

description: Library name: RNA_04

value: Donor + B2M RNP, Mock


title: G7883_treated_parental_H226_cells_rep2 (Micro-Capture C)

description: Library name: Parental_G7883_rep2


title: U2OS, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_U2OS_Replicate1

value: Osteosarcoma


title: BOBYXJO

status: Public on Feb 08 2025

city: Basel

first: Francis

last: Jacob

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel and University of Basel

description: Library name: Sample182

data_processing:
The pipeline encompassed several key steps, beginning with initial quality assessment and adapter trimming of raw reads. Processed reads were then mapped to the GRCh38 primary assembly (GRCh38.primary_assembly.genome.fa, obtained from the Gencode website) using STAR aligner102. The alignment was guided by the Gencode v41 primary annotation (gencode.v41.primary_assembly.annotation.gtf).
Following alignment, Salmon103 was employed to quantify transcript abundances, with the --rf-stranded (reverse/forward) parameter specified to account for the stranded nature of the TruSeq library preparation, ensuring correct strand-specific quantification of transcripts. Throughout the pipeline, several quality control measures were implemented.
These included FastQC for assessment of sequence quality metrics, featureCounts for quantification of reads mapped to different genomic features and biotypes (e.g., protein-coding genes, lncRNAs, miRNAs), and DESeq2 for Principal Component Analysis (PCA) and sample similarity analysis to identify potential batch effects or outliers. Additionally, Picard MarkDuplicates was used to identify PCR and optical duplicates (duplicates were marked but not removed), Samtools generated alignment statistics and quality metrics, and RSeQC provided comprehensive quality control of alignment results, including read distribution, gene body coverage, and splice junction analysis.
Assembly: GRCh38
Supplementary files format and content: txt

extract_protocol:
Biobanked RNAlater (Thermo Fisher Scientific, cat. No. AM7021) samples were homogenized, and an average weight aliquot of 54mg was used for total RNA isolation. RNA extraction was performed using the RNeasy Plus Universal Mini Kit (50) (Qiagen, cat. no. 73404), incorporating of PhasemakerTM Tubes (Thermo Fisher Scientific, cat. No. A33248). RNA sample quantification was performed using an Invitrogen Qubit 4 fluorometer with the Invitrogen Qubit RNA BR Assay Kit, while RNA sample integrity was assessed using an Agilent Fragment Analyzer with the RNA Kit. The mean RIN of the entire cohort was 8.6 ranging from 6.2 to 10.
RNA-seq libraries were prepared using 200 ng of total RNA and the Illumina TruSeq Stranded mRNA Library Prep kit, following the manufacturer's protocol. Library quality control and quantification were performed using an Invitrogen Qubit 4 fluorometer with the Invitrogen Qubit dsDNA 1X HS Assay kit for quantification, and an Agilent Fragment Analyzer with the Agilent NGS Fragment Kit for quality control. Sequencing was performed on an Illumina NovaSeq 6000 platform, generating 100 bp paired-end reads (Health 2030 Genome Center, Geneva, Switzerland).
RNA-seq data were processed and analyzed using the nf-core/rnaseq pipeline (version 3.8.1)101.

tag: disease

value: HGSOC

tag: tissue tag

value: OF

tag: time

tag: figo stage

value: IIIC

tag: batch


title: G7883_treated_parental_H226_cells_rep1 (Micro-Capture C)

description: Library name: Parental_G7883_rep1


title: DMSO_treated_parental_H226_cells_rep2 (Micro-Capture C)

description: Library name: Parental_DMSO_rep2


title: BOBOTLI

description: Library name: Sample183

value: OM


title: BOBEKOO

description: Library name: Sample181


title: BOBHAXK

description: Library name: Sample180

source_name: Ascites

value: Ascites

value: L


title: BMT-CTN-179_Bag_CD3

description: Library name: BMT-CTN-179_Bag_CD3

value: Blood


title: BOBUEXL

description: Library name: Sample177

value: IV


title: BOBBVRD

description: Library name: Sample178

value: cOM


title: BOBIYXQ

description: Library name: Sample176


title: BOBAGEW

description: Library name: Sample175


title: BOBVDSC

description: Library name: Sample174


title: BOBZZKE

description: Library name: Sample173


title: BOBBATD

description: Library name: Sample172


title: BOBTNSE

description: Library name: Sample171

value: LN


title: BOBNFIA

description: Library name: Sample170


title: G7883_resistant_H226_cells_rep1 (Micro-Capture C)

description: Library name: Resistant_G7883_rep1


title: BOBLUNE

description: Library name: Sample169


title: BOBPHUC

description: Library name: Sample168


title: BOBQKGS

description: Library name: Sample165


title: BOBJILH

description: Library name: Sample163


title: BOBGDJQ

description: Library name: Sample167


title: BOBGYOS

description: Library name: Sample164


title: BOBPGDM

description: Library name: Sample161


title: BOBWZCF

description: Library name: Sample166


title: BOBIHYI

description: Library name: Sample157

value: R

value: IIIB


title: BOBTACH

description: Library name: Sample158


title: BOBPVBH

description: Library name: Sample155


title: BOBGMTN

description: Library name: Sample160


title: BOBNLZH

description: Library name: Sample156


title: BOBFIHA

description: Library name: Sample154


title: BOBJOWV

description: Library name: Sample179


title: BOBGAFM

description: Library name: Sample151


title: BOBODMC

description: Library name: Sample150


title: BOBZDMH

description: Library name: Sample149


title: BOBLYMT

description: Library name: Sample162

value: T


title: DMSO_treated_parental_H226_cells_rep1 (Micro-Capture C)

description: Library name: Parental_DMSO_rep1

value: Lung

value: Mesothelioma


title: BOBYYKW

description: Library name: Sample148


title: BOBUNHX

description: Library name: Sample146


title: BOBUFJM

description: Library name: Sample153


title: BOBBAIW

description: Library name: Sample159


title: BOBZZQW

description: Library name: Sample152


title: BOBYMGH

description: Library name: Sample143

value: cD


title: BOBHZTN

description: Library name: Sample142

value: P


title: BOBWEQZ

description: Library name: Sample147

value: HGSOC


title: BOBCVPV

description: Library name: Sample144

value: cP


title: BOBKVAV

description: Library name: Sample139

value: OF


title: BOBDVZW

description: Library name: Sample138


title: BOBWSBX

description: Library name: Sample137


title: BOBBPWS

description: Library name: Sample134


title: BOBJSQG

description: Library name: Sample135


title: BOBCOTA

description: Library name: Sample132

value: OM


title: BOBWHJE

description: Library name: Sample129

value: IIIC


title: BOBQWFH

description: Library name: Sample130


title: BOBTFOQ

description: Library name: Sample131


title: BOBEKOT

description: Library name: Sample133


title: BOBUYGS

description: Library name: Sample128


title: BOBBXHK

description: Library name: Sample127


title: BOBNNFR

description: Library name: Sample126

value: Ascites

value: L


title: BOBBYFT

description: Library name: Sample125

value: IV


title: BOBKSJW

description: Library name: Sample124


title: BOBPPIK

description: Library name: Sample123

value: cOM


title: BOBZEGT

description: Library name: Sample122


title: BOBOPSH

description: Library name: Sample121


title: BOBXALR

description: Library name: Sample145


title: BOBENVO

description: Library name: Sample120

value: M


title: BOBOTVU

description: Library name: Sample118


title: BOBQXGO

description: Library name: Sample119


title: BOBDIYD

description: Library name: Sample117


title: BOBCABB

description: Library name: Sample141


title: BOBJYFS

description: Library name: Sample116


title: BOBPXPT

description: Library name: Sample115


title: BOBFLDU

description: Library name: Sample136


title: BOBXSRP

description: Library name: Sample140


title: BOBXCNH

description: Library name: Sample113


title: BOBSXWD

description: Library name: Sample112


title: BOBFDWJ

description: Library name: Sample114


title: BOBKWFL

description: Library name: Sample111


title: BOBFJZI

description: Library name: Sample110


title: BOBHRER

description: Library name: Sample109


title: BOBGRQT

description: Library name: Sample107


title: BOBKDXL

description: Library name: Sample105


title: BOBOSCN

description: Library name: Sample103

value: B


title: BOBUFPZ

description: Library name: Sample102


title: BOBAXAP

description: Library name: Sample104


title: BOBIUKL

description: Library name: Sample108


title: BOBMJJX

description: Library name: Sample106


title: BOBQLUB

description: Library name: Sample100


title: BOBVJPE

description: Library name: Sample98


title: BOBRLOS

description: Library name: Sample101


title: BOBDRAP

description: Library name: Sample99

value: S


title: BOBSMMS

description: Library name: Sample97


title: BOBHSJW

description: Library name: Sample95


title: BOBGJQR

description: Library name: Sample94


title: BOBKQLB

description: Library name: Sample96


title: BOBMTFT

description: Library name: Sample92

value: D


title: BOBTIPH

description: Library name: Sample93


title: BOBJHJZ

description: Library name: Sample91


title: BOBYRQF

description: Library name: Sample90


title: BOBLCYR

description: Library name: Sample88

value: R


title: BOBIKGM

description: Library name: Sample85


title: BOBLBUQ

description: Library name: Sample87


title: BOBOVCS

description: Library name: Sample89


title: BOBEKAS

description: Library name: Sample86


title: BOBBVZL

description: Library name: Sample84


title: BOBIGID

description: Library name: Sample83


title: BOBPPCD

description: Library name: Sample80


title: BOBCRBE

description: Library name: Sample77


title: BOBBOWC

description: Library name: Sample82


title: BOBFJJF

description: Library name: Sample79


title: BOBLYMJ

description: Library name: Sample78


title: BOBBMXQ

description: Library name: Sample76


title: BOBHWYU

description: Library name: Sample70


title: BOBGIPQ

description: Library name: Sample72

value: IIB


title: BOBAEUY

description: Library name: Sample69


title: BOBABDJ

description: Library name: Sample68


title: BOBTCYN

description: Library name: Sample67


title: BOBRQEY

description: Library name: Sample66


title: BOBZUGU

description: Library name: Sample64


title: BOBNFAZ

description: Library name: Sample62


title: BOBTXYI

description: Library name: Sample60


title: BOBZITF

description: Library name: Sample65


title: BOBJQZQ

description: Library name: Sample63


title: BOBCWCP

description: Library name: Sample81


title: BOBAYSJ

description: Library name: Sample56


title: BOBKYTZ

description: Library name: Sample58


title: BOBUVMK

description: Library name: Sample57


title: BOBGYWZ

description: Library name: Sample59


title: BOBHJYH

description: Library name: Sample52


title: BOBRUIG

description: Library name: Sample53


title: BOBVWZK

description: Library name: Sample55


title: BOBGZJX

description: Library name: Sample54


title: BOBQABQ

description: Library name: Sample75


title: BOBMRJF

description: Library name: Sample71


title: BOBUMUH

description: Library name: Sample73


title: BOBUGTR

description: Library name: Sample74


title: BOBDMNU

description: Library name: Sample50


title: BOBKMNF

description: Library name: Sample48

value: IIIB


title: BOBYHLZ

description: Library name: Sample49


title: BOBKYWH

description: Library name: Sample46


title: BOBCDTL

description: Library name: Sample44


title: BOBNUMB

description: Library name: Sample47


title: BOBVQJT

description: Library name: Sample45


title: BOBXTOG

description: Library name: Sample40


title: BOBKPTH

description: Library name: Sample43


title: BOBDAHT

description: Library name: Sample41


title: BOBVZIG

description: Library name: Sample38


title: BOBIEWN

description: Library name: Sample61


title: BOBBPMS

description: Library name: Sample39


title: BOBNSYG

description: Library name: Sample37


title: BOBQWKG

description: Library name: Sample32

value: cR


title: BOBFPXU

description: Library name: Sample35

value: HGSOC


title: BOBNSOX

description: Library name: Sample31


title: BOBNVCH

description: Library name: Sample30


title: BOBLTNQ

description: Library name: Sample29


title: BOBNGJE

description: Library name: Sample34

value: P


title: BOBOWZF

description: Library name: Sample33

value: OF


title: BOBPWAH

description: Library name: Sample51


title: BOBSJRJ

description: Library name: Sample27


title: BOBOUEH

description: Library name: Sample26


title: BOBHPLY

description: Library name: Sample23

value: OM


title: BOBCWVZ

description: Library name: Sample25

value: IIIC


title: BOBNCNG

description: Library name: Sample24


title: BOBLBJV

description: Library name: Sample28


title: BOBYPXV

description: Library name: Sample42


title: BOBMEVS

description: Library name: Sample20


title: BOBNYWC

description: Library name: Sample22


title: BOBKHVV

description: Library name: Sample17

value: IVB


title: BOBGPQV

description: Library name: Sample18


title: BOBZPTF

description: Library name: Sample16


title: BOBRQBD

description: Library name: Sample19


title: BOBYTVY

description: Library name: Sample21

value: LN


title: BOBWKDL

description: Library name: Sample36

value: Ascites

value: L


title: BOBAYYF

description: Library name: Sample14

value: cOM


title: BOBHLMR

description: Library name: Sample13


title: BOBWUGU

description: Library name: Sample11


title: BOBGIIJ

description: Library name: Sample10


title: BOBLOJM

description: Library name: Sample9

value: IV


title: BOBFYBE

description: Library name: Sample12


title: BOBUOIO

description: Library name: Sample15


title: BOBQKGU

description: Library name: Sample8


title: BOBHZGJ

description: Library name: Sample6


title: BOBYYIC

description: Library name: Sample5


title: BOBJRVK

description: Library name: Sample2


title: BOBYZES

description: Library name: Sample4


title: BOBOSNC

description: Library name: Sample1


title: BOBETNV

description: Library name: Sample3


title: Sample_J_larry, KO

status: Public on Feb 03 2025

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: Sample_J_larry
J_star_unfiltered_counts.h5ad
J_star_unfiltered_features.h5ad

data_processing:
Unfiltered counts and feature counts (LARRY barcodes) generated for each library using STAR. Feature counts have been very slightly corrected for an edge case that affects about 1 in 10,000 counts. QC has been added and uploaded for the feature assignments. Feature assignment has also been done directly from the scRNA-seq expression as a control for the targeted sequence method (which is the main value in the features counts file). These are available in the 'expression' layer. Assignments have been provided for the features. These follow the original MSK criterion (minimum 10 counts - second best count no more than half of maximum). A second less restrictive assignment has also been provided using a minimum 4 counts - second best count no more than half of maximum). These are provided as obs 'feature-10' and 'feature-4'. These are provided as a convenience - filtering can still be done using whatever criteria the user wishes from the feature_counts file data.
https://github.com/morphic-bio/process_features
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: Unfiltered counts and feature counts per library as h5ad files. Zip folder includes QC files (.txt and .png) for expression feature assignments and targeted feature assignments.

source_name: ESC

extract_protocol: Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1

value: H1_J_PP, HUES8_J_PP

value: ESC

tag: editing strategy

value: enhancer, gene body

tag: altered gene_symbol

value: PDX1, HES1, NEUROD1, PAX6, NKX2-2, ARX, GATA6, GATA4, FOXA2, FOXA1, RFX6, GLIS3, HHEX, UBA6, OTUD5, TADA2B, KDM2B, GSC, ONECUT1, MNX1, TET1, TET2, TET3, NANOG, BCOR, NEUROG3, BMPR1A, TLE3, NKX6-1, PBX1, QSER1, PROSER1, HNF4A

tag: time (day)

tag: model system

value: pancreatic progenitor (stage 4), pancreatic progenitor (stage 4)

tag: parental cell_line

value: H1, HUES8

tag: pooled samples


title: Sample_H_larry, KO

description:
Library name: Sample_H_larry
H_star_unfiltered_counts.h5ad
H_star_unfiltered_features.h5ad

value: H1_H_DE, HUES8_H_DE

value: Definitive endoderm (stage 1), Definitive endoderm (stage 1)


title: Sample_L_larry, KO

description:
Library name: Sample_L_larry
L_1_star_unfiltered_counts.h5ad
L_1_star_unfiltered_features.h5ad
L_2_star_unfiltered_counts.h5ad
L_2_star_unfiltered_features.h5ad

value: H1_L_3DEC, HUES8_L_3DEC

value: immature SC-islet (stage 5), immature SC-islet (stage 5)


title: Sample_F_larry, WT

description:
Library name: Sample_F_larry
F_star_unfiltered_counts.h5ad
F_star_unfiltered_features.h5ad

value: Not applicable

value: ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), stage 5 day 2, stage 5 day 4, immature SC-islet (stage 5), stage 6 day 3, mature SC-islet (stage 6)


title: Sample_G_larry, KO

description:
Library name: Sample_G_larry
G_1_star_unfiltered_counts.h5ad
G_1_star_unfiltered_features.h5ad
G_2_star_unfiltered_counts.h5ad
G_2_star_unfiltered_features.h5ad

value: H1_G_ESC, HUES8_G_ESC

value: ESC (stage 0), ESC (stage 0)


title: Sample_I_larry, KO

description:
Library name: Sample_I_larry
I_star_unfiltered_counts.h5ad
I_star_unfiltered_features.h5ad

value: H1_I_PFG, HUES8_I_PFG

value: posterior foregut (stage 3), posterior foregut (stage 3)


title: Sample_D_larry, WT

description:
Library name: Sample_D_larry
D_star_unfiltered_counts.h5ad
D_star_unfiltered_features.h5ad


title: Sample_E_larry, WT

description:
Library name: Sample_E_larry
E_star_unfiltered_counts.h5ad
E_star_unfiltered_features.h5ad


title: Sample_B_larry, WT

description:
Library name: Sample_B_larry
B_star_unfiltered_counts.h5ad
B_star_unfiltered_features.h5ad

value: ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), stage 5 day 1 , stage 5 day 3, stage 5 day 5, immature SC-islet (stage 5), stage 6 day 7


title: Sample_A_larry, WT

description:
Library name: Sample_A_larry
A_star_unfiltered_counts.h5ad
A_star_unfiltered_features.h5ad


title: Sample_H_transcriptome, KO

description:
Library name: Sample_H_transcriptome
H_star_unfiltered_counts.h5ad
H_star_unfiltered_features.h5ad


title: Sample_G_transcriptome, KO

description:
Library name: Sample_G_transcriptome
G_1_star_unfiltered_counts.h5ad
G_1_star_unfiltered_features.h5ad
G_2_star_unfiltered_counts.h5ad
G_2_star_unfiltered_features.h5ad


title: Sample_F_transcriptome, WT

description:
Library name: Sample_F_transcriptome
F_star_unfiltered_counts.h5ad
F_star_unfiltered_features.h5ad


title: Sample_E_transcriptome, WT

description:
Library name: Sample_E_transcriptome
E_star_unfiltered_counts.h5ad
E_star_unfiltered_features.h5ad


title: Sample_I_transcriptome, KO

description:
Library name: Sample_I_transcriptome
I_star_unfiltered_counts.h5ad
I_star_unfiltered_features.h5ad


title: Sample_L_transcriptome, KO

description:
Library name: Sample_L_transcriptome
L_1_star_unfiltered_counts.h5ad
L_1_star_unfiltered_features.h5ad
L_2_star_unfiltered_counts.h5ad
L_2_star_unfiltered_features.h5ad


title: BOBISDN

description: Library name: Sample7

tag: tissue

value: HGSOC

value: OF

value: IV


title: Sample_J_transcriptome, KO

description:
Library name: Sample_J_transcriptome
J_star_unfiltered_counts.h5ad
J_star_unfiltered_features.h5ad

value: H1_J_PP, HUES8_J_PP

value: ESC

value: enhancer, gene body

value: PDX1, HES1, NEUROD1, PAX6, NKX2-2, ARX, GATA6, GATA4, FOXA2, FOXA1, RFX6, GLIS3, HHEX, UBA6, OTUD5, TADA2B, KDM2B, GSC, ONECUT1, MNX1, TET1, TET2, TET3, NANOG, BCOR, NEUROG3, BMPR1A, TLE3, NKX6-1, PBX1, QSER1, PROSER1, HNF4A


title: Sample_A_transcriptome, WT

description:
Library name: Sample_A_transcriptome
A_star_unfiltered_counts.h5ad
A_star_unfiltered_features.h5ad

value: H1, HUES8


title: Sample_C_transcriptome, WT

description:
Library name: Sample_C_transcriptome
C_star_unfiltered_counts.h5ad
C_star_unfiltered_features.h5ad

value: ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), stage 5 day 2, stage 5 day 4, immature SC-islet (stage 5), stage 6 day 3, stage 6 day 8


title: PA_QN302_BG4_C&T_biol rep 3

status: Public on Jan 31 2025

city: Padova

first: Beatrice

last: Tosoni

state: Padova

address: via Aristide Gabelli 63

country: Italy

institute: University ofPadova

data_processing:
Sequencing data were analyzed with the open-source web platform Galaxy (www.usegalaxy.org) together with R (version 4.2.1 – RStudio, version 2022.07.0). Reads were aligned to the human reference genome (GRCh38) using Bowtie2 (v2.5.0)31 by FastQC quality control (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). G4 peaks were called with MACS2 (v2.2.7.1) (ref) (-gsize 2.7e9 -bw 150 -qvalue 0.05).
Assembly: hg38
Supplementary files format and content: Bigwig files.
Library strategy: CUT&Tag

growth_protocol: The human WDLPS cell line, named WD, was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution. The two patient-derived DDLPS cell lines, named DD-1 and DD-2 respectively, were cultured in DMEM/F-12 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution. The normal human subcutaneous pre-adipocytes, called PA, were cultured in PBM-2 medium supplemented with Gentamicin, 7.5 mM L-glutamine, and 2% fetal bovine serum.

extract_protocol:
DNA was extracted by phenol and chloroform solution, followed by precipitatation step in cold 100% ethanol.
The library were constructed with pA-Tn5 complex, amplified by PCR and size selected with Ampure XP beads.

treatment_protocol: Cells were treated with QN-302 (0.8 μM) for 4 hours.


title: Sample_B_transcriptome, WT

description:
Library name: Sample_B_transcriptome
B_star_unfiltered_counts.h5ad
B_star_unfiltered_features.h5ad


title: DD2_QN302_BG4_C&T_biol rep 2

source_name: LS-BZ-1 (DDLPS)

value: LS-BZ-1 (DDLPS)

value: human de-differentiated liposarcoma


title: PA_QN302_BG4_C&T_biol rep 2

value: normal human subcutaneous pre-adipocytes


title: DD2_QN302_BG4_C&T_biol rep 1


title: PA_QN302_BG4_C&T_biol rep 1


title: Sample_D_transcriptome, WT

description:
Library name: Sample_D_transcriptome
D_star_unfiltered_counts.h5ad
D_star_unfiltered_features.h5ad

value: Not applicable

value: ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), ESC (stage 0), Definitive endoderm (stage 1), primitive gut tube (stage 2), posterior foregut (stage 3), stage 4 day 1 , stage 4 day 2, pancreatic progenitor (stage 4), stage 5 day 2, stage 5 day 4, immature SC-islet (stage 5), stage 6 day 3, mature SC-islet (stage 6)


title: DD1_QN302_BG4_C&T_biol rep3

source_name: LS-GD-1 (DDLPS)

value: LS-GD-1 (DDLPS)


title: DD2_QN302_BG4_C&T_biol rep 3


title: Sample_C_larry, WT

description:
Library name: Sample_C_larry
C_star_unfiltered_counts.h5ad
C_star_unfiltered_features.h5ad


title: WD_QN302_BG4_C&T_biol rep 2

value: human well-differentiated liposarcoma


title: WD_QN302_BG4_C&T_biol rep 1


title: DD1_QN302_BG4_C&T_biol rep 1


title: DD1_QN302_BG4_C&T_biol rep 2


title: PA_QN302_RNAseq_biolrep2

data_processing:
Sequencing data were analyzed with the open-source web platform Galaxy (www.usegalaxy.org) together with R (version 4.2.1 – RStudio, version 2022.07.0). Reads were aligned to the human reference genome (GRCh38) using Bowtie2 (v2.5.0)31 by FastQC quality control (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). G4 peaks were called with MACS2 (v2.2.7.1) (ref) (-gsize 2.7e9 -bw 150 -qvalue 0.05).
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts.

growth_protocol: The human WDLPS cell line, named WD, was cultured in RPMI-1640 medium  supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution. The two patient-derived DDLPS cell lines, named DD-1 and DD-2 respectively, were cultured in  DMEM/F-12 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution. The normal human subcutaneous pre-adipocytes, called PA, were cultured in PBM-2 medium supplemented with Gentamicin, 7.5 mM L-glutamine, and 2% fetal bovine serum.

extract_protocol:
RNA was extracted with GeneJet RNA Purification kit (K0731, Thermo) and subjected to TURBO-DNase digestion..
The library were constructed with 3'mRNA Lexogen kit (Illumina).

value: QN-302 treatment


title: PA_QN302_RNAseq_biolrep3


title: PA_QN302_RNAseq_biolrep1


title: PA_ND_RNAseq_biolrep2

value: untreated


title: PA_ND_RNAseq_biolrep1


title: DD2_ND_RNAseq_biolrep3


title: DD2_QN302_RNAseq_biolrep1


title: DD2_QN302_RNAseq_biolrep3


title: DD2_ND_RNAseq_biolrep2


title: DD2_QN302_RNAseq_biolrep2


title: DD1_QN302_RNAseq_biolrep3


title: DD1_QN302_RNAseq_biolrep2


title: DD1_ND_RNAseq_biolrep2


title: WD_QN302_RNAseq_biolrep2


title: WD_QN302_RNAseq_biolrep1


title: WD_ND_RNAseq_biolrep2


title: DD1_QN302_RNAseq_biolrep1


title: DD2_ND_RNAseq_biolrep1


title: WD_ND_RNAseq_biolrep1


title: PA_ND_RNAseq_biolrep3


title: PA_BG4_C&T_biol rep 2


title: DD2_BG4_C&T_biol rep 2


title: PA_BG4_C&T_biol rep 3


title: DD1_ND_RNAseq_biolrep3


title: PA_BG4_C&T_biol rep 1


title: DD2_BG4_C&T_biol rep 3


title: DD1_ND_RNAseq_biolrep1


title: DD2_BG4_C&T_biol rep 1


title: DD1_BG4_C&T_biol rep 1


title: WD_QN302_BG4_C&T_biol rep 3


title: DD1_BG4_C&T_biol rep 2


title: WD_BG4_C&T_biol rep 3


title: DD1_BG4_C&T_biol rep3


title: WD_BG4_C&T_biol rep 1


title: WD_BG4_C&T_biol rep 2


title: A498_1G11.B05_B

status: Public on Jan 17 2025

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

data_processing:
STAR
HTseq
gencode_v22
Assembly: hg38
Supplementary files format and content: HTseq raw counts

source_name: kidney

growth_protocol: All cell lines used in these studies were cultured following protocols/conditions provided by the American Type Culture Collection (ATCC) where available. Specifically, the 786-O cell lines were cultured in RPMI 1640 media (ATCC 30-2001) supplemented with 10% FBS, and 1% Pen/Strep (ThermoFisher # 15070-063). A498 cell lines were cultured in Eagle's Minimum Essential Medium (ATCC #30-2003) supplemented with 10% FBS and 1% Pen/Strep. RPTEC were cultured in DMEM:F12 media (ThermoFisher, catalog #11320-082) supplemented with 10%FBS, MEM non-essential amino acids (ThermoFisher, catalog #11140-050), sodium pyruvate (ThermoFisher, catalog #11360-070), RPTEC growth kit (ATCC, catalog #ACS-4007), and 250 mg/ml G418 (ThermoFisher, catalog #10131-035) for maintaining selection of hTERT expression. The HAP1 cell lines were purchased from Horizon Discovery and cultured in Iscove's Modified Dulbecco's Medium (ThermoFisher #12440-053) supplemented with 10% FBS, and 1% Pen/Strep.

extract_protocol:
Qiagen Rneasy
Illumina TruSeq Stranded mRNA

treatment_protocol: Packaging of lentiviral particles was carried out by lipid-based transient transfection 24hrs following plating of 293T cells (plating density ~1e5 cells/cm2). Lentiviral transfer vectors were mixed with 2nd generation packaging  plasmids: psPAX2 (Addgene #12260) and pMD2.g (Addgene #12259) at a molar ratio of 3:2:1 and delivered to 293T cells using JetOptimus transfection reagent (Polyplus # 101000051) at a DNA:lipid ratio of 1:2. Lentiviral supernatant was collected 72hrs post-transfection and filtered through a 0.45 nm polyethersulfone syringe filter (FisherScientific 13-100-107). When required, lentivirus was concentrated by ultracentrifugation (25,000 RPM; 2hrs; 4°C) and resuspended in 0.5 mL DMEM. Lentiviral transduction of target cells was carried out at a MOI of 1-5 depending on the application and carried out for 48hrs before removal of the lentivirus and initiation of drug selection. Selection for gene targeting, dCas9-KRAB expression, and 3XFLAG-SETD2 expression was carried out with 5 mg/mL  Blasticidin (ThermoFisher #A1113903). Selection for CRISPRi sgRNA expression was carried out with 1.5 mg/mL Puromycin (ThermoFisher # A1113802) following lentiviral transduction. Tamoxifen (Sigma # T2859) was resuspended in methanol and cells treated at 1 mM for 24 hrs to induce Cre-lox recombination. BT5 and MK1775 (Selleckchem #S1525) were resuspended in DMSO with cells treated at the concentration indicated.  For competition studies, wildtype and mutant isogenic cell lines were labeled with EGFP-H2A or mCherry-H2A fusion genes respectively via lentiviral transduction, and subsequently mixed at a 1:1 ratio for treatment with increasing concentration of drug.

value: kidney

value: Rescue


title: WD_QN302_RNAseq_biolrep3


title: WD_ND_RNAseq_biolrep3


title: A498_1G11.A01_A


title: A498_1G11.A01_B


title: X786O_WT_Vehicle_B

value: WT

value: Vehicle


title: X786O_WT_Vehicle_A


title: X786O_WT_d4_5uM_BT5_B

value: 5uM BT5


title: X786O_WT_d4_5uM_BT5_A


title: X786O_38E_Vehicle_B


title: X786O_38E_d4_5uM_BT5_B


title: X786O_38E_d4_5uM_BT5_A


title: RPTEC_WT_Pa_rep2

value: RPTEC


title: RPTEC_Mut_G5_rep1


title: RPTEC_WT_Pa_rep1


title: RPTEC_Mut_G5_rep2


title: RPTEC_Mut_E1_rep1


title: X786O_38E_Vehicle_A


title: RPTEC_Mut_E1_rep2


title: A498_Pa_rep1


title: 786O_38E_NSD2_B


title: X786_O_WT_Pa_rep2


title: A498_1G11.B05_A


title: 786O_38E_NSD2_A


title: X786_O_WT_Pa_rep1


title: X786_O_Mut_38F_rep2


title: X786_O_Mut_38E_rep2


title: A498_SETD2-HDR_dCas9-KRAB_clone_6_sgNSD1_day12_A


title: X786_O_Mut_38F_rep1


title: A498_SETD2-HDR_dCas9-KRAB_clone_6_sgCTRL_day12_A


title: A498_SETD2-HDR_dCas9-KRAB_clone_6_sgNSD1_day12_B


title: A498_parent_dCas9-KRAB_clone_3_sgCTRL_day12_A


title: A498_parent_dCas9-KRAB_clone_3_sgNSD1_day12_B


title: A498_parent_dCas9-KRAB_clone_3_sgNSD1_day12_A


title: 786-O_parent_dCas9-KRAB_clone_6_sgCTRL_day9_B


title: A498_Pa_rep2


title: 786-O_parent_dCas9-KRAB_clone_6_sgNSD1_day9_A


title: 786-O_parent_dCas9-KRAB_clone_6_sgNSD1_day9_B


title: 786-O_38F_dCas9-KRAB_clone_11_sgCTRL_day9_B


title: 786-O_38F_dCas9-KRAB_clone_11_sgNSD1_day9_B


title: 786-O_38F_dCas9-KRAB_clone_11_sgCTRL_day9_A


title: A498_3xFLAG_clone3_H3K36me3_B

data_processing:
ChIP-seq was mapped and align using Spiker (https://github.com/liguowang/spiker) which uses a custom human + drosophila index for bowtie2 to parse out human and fly read ratios to scale read counts. The scaling factor was applied prior to DESeq2 to call differential peaks. Gene and peak significance values were cutoff at log2 fold change > |1| and adjusted p-value <0.05.
Spiker
MACS2
NOTE: there are some processed files with 0kb. These are all scaled counts, so those files resulted in zero called peaks, thus 0kb output.
Assembly: hg38
Supplementary files format and content: peak calls

extract_protocol:
ChIP-seq libraries were prepared as described previously (PMID: 37418588). In brief, S2 drosophila chromatin  was spiked into each chromatin prep before immunoprecipitation .
amples were fixed with 1% paraformaldehyde and digested with micrococcal nuclease to isolate nucleosomes. Sonication was performed using a Diagenode Bioruptor. Chromatin input was measured using a Qubit Fluorometer (Thermo Fisher).

tag: histone mark

tag: replicate

value: B


title: A498_3xFLAG_clone3_Input_B

tag: cell line

value: Input


title: A498_3xFLAG_clone3_Input_A

value: A

tag: genotype


title: A498_SETD2-HDR_dCas9-KRAB_clone_6_sgCTRL_day12_B


title: X786_O_Mut_38E_rep1


title: A498_3xFLAG_clone2_Input_B


title: A498_3xFLAG_clone2_Input_A


title: A498_3xFLAG_clone2_H3K36me3_A


title: 786-O_38E_dCas9-KRAB_clone_5_sgCTRL_day9_B


title: 786-O_38F_dCas9-KRAB_clone_11_sgNSD1_day9_A


title: A498_parent_dCas9-KRAB_clone_3_sgCTRL_day12_B


title: A498_parent_H3K36me3_A


title: 786-O_38E_dCas9-KRAB_clone_5_sgCTRL_day9_A


title: A498_parent_Input_A


title: A498_3xFLAG_clone2_H3K36me3_B


title: 786-O_parent_dCas9-KRAB_clone_6_sgCTRL_day9_A


title: RPTEC_WT_H3K36me3_B


title: A498_parent_Input_B


title: 786-O_38E_dCas9-KRAB_clone_5_sgNSD1_day9_A


title: A498_parent_H3K36me3_B


title: RPTEC_WT_H3K36me3_A


title: RPTEC_WT_Input_B


title: A498_3xFLAG_clone3_H3K36me3_A


title: RPTEC_WT_Input_A


title: 786-O_38E_BirA-SETD2_clone_E5_clonal_B


title: RPTEC_G5_H3K36me3_B


title: RPTEC_G5_H3K36me3_A


title: X786Ocl2 DMSO rep 2

extract_protocol:
Trizol
Illumina TruSeq Stranded mRNA

treatment_protocol: STM2457, 20uM, 3 days

tag: cell type

value: Clear cell renal cell carcinoma

value: SETD2 WT

tag: treatment


title: 786-O_38E_BirA-SETD2_clone_E5_clonal_A


title: RPTEC_G5_Input_B


title: X786Ocl2 DMSO rep 1


title: RPTEC_E1_Input_B


title: RPTEC_E1_Input_A


title: RPTEC_E1_H3K36me3_B


title: X786Ocl2 STM2457 rep 2


title: RPTEC_E1_H3K36me3_A


title: 786O_38F_Batch3_H3K36me2_B


title: X786Ocl2 STM2457 rep 1


title: 786-O_38E_dCas9-KRAB_clone_5_sgNSD1_day9_B


title: 786O_38F_Batch3_H3K36me2_A


title: X786OWT DMSO rep 1


title: X786OWT DMSO rep 2


title: 786O_38F_Batch3_Input_A


title: 786O_38F_Batch3_Input_B


title: X786OWT STM2457 rep 2


title: 786O_38E_Batch3_Input_A


title: 786O_38E_Batch3_H3K36me2_A


title: X786OWT STM2457 rep 1


title: 786O_WT_Batch3_H3K36me2_B


title: 786O_WT_Batch3_Input_B


title: RPTEC_G5_Input_A


title: 786O_WT_Batch3_H3K36me2_A


title: X786Ocl2 sgCas9 CTRL rep 2

value: SETD2 KO


title: 786O_WT_H3K36me3_B


title: X786Ocl2 sgCas9 CTRL rep 1


title: 786O_WT_Input_B


title: 786O_WT_Batch3_Input_A


title: X786Ocl2 METTL3KO C2 rep 2


title: 786O_38E_Batch3_H3K36me2_B


title: 786O_WT_H3K36me3_A


title: X786Ocl2 METTL3KO C2 rep 1


title: 786O_38E_Batch3_Input_B


title: 786O_38F_Input_B


title: X786Ocl2 METTL3KO C1 rep 2


title: 786O_38F_Input_A


title: 786O_38E_H3K36me3_A


title: 786O_WT_Input_A


title: X786Ocl2 METTL3KO C1 rep 1


title: X786OWT sgCas9 CTRL rep 2


title: 786O_38E_H3K36me3_B


title: 786O_38E_Input_A


title: 786O_parent_sgNSD2_K36me2_B


title: 786O_38E_Input_B


title: X786OWT sgCas9 CTRL rep 1


title: 786O_parent_sgNSD2_K36me3_A


title: 786O_parent_sgNSD2_K36me3_B


title: 786O_38F_H3K36me3_B


title: X786OWT METTL3KO A2 rep 1


title: 786O_parent_sgNSD2_Input_A


title: X786OWT METTL3KO A1 rep 2


title: 786O_parent_sgNSD2_K36me2_A


title: 786O_parent_sgNSD1_K36me2_B


title: 786O_parent_sgNSD1_K36me3_B


title: 786O_38F_H3K36me3_A


title: X786OWT METTL3KO A1 rep 1


title: 786O_parent_sgNSD1_K36me3_A


title: RPTEC cl1 SETD2resc rep 2 Input

data_processing:
STAR
HT-seq
MACS2
Assembly: hg38
Supplementary files format and content: Tab delimited peak scores, bed
Library strategy: MeRIP-seq

growth_protocol: 786-O RPMI1640 + 10% FBS, RPTEC DMEM f12 + RPTEC growth kit + 10% FBS

extract_protocol:
Trizol
SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian

value: Renal proximal tubule epithelial cell

value: SETD2 resc


title: 786O_parent_sgNSD1_Input_A


title: RPTEC cl1 SETD2resc rep 1 Input


title: 786O_parent_sgCTRL_K36me3_B


title: 786O_parent_sgCTRL_K36me2_B


title: 786O_parent_sgCTRL_Input_B


title: RPTEC SETD2KO cl2 rep 1 Input


title: 786O_parent_sgCTRL_K36me2_A


title: RPTEC SETD2KO cl2 rep 2 Input


title: 786O_parent_sgCTRL_K36me3_A


title: 786O_parent_sgNSD2_Input_B


title: X786OWT METTL3KO A2 rep 2


title: 786O_parent_sgCTRL_Input_A


title: 786O_ChromHMM_38E_3xFLAG_K36me3_B


title: 786O_ChromHMM_38E_3xFLAG_K36me3_A


title: RPTEC WT rep 2 Input


title: RPTEC SETD2KO cl1 rep 1 Input


title: RPTEC SETD2KO cl1 rep 2 Input


title: 786O_ChromHMM_38E_3xFLAG_K36me2_B


title: 786O_ChromHMM_38E_3xFLAG_K36me2_A


title: 786O_ChromHMM_38E_3xFLAG_Input_B


title: 786O_parent_sgNSD1_Input_B


title: 786O_ChromHMM_38E_3xFLAG_Input_A


title: 786O_ChromHMM_38E_H3K36me3_B


title: 786O_ChromHMM_38E_H3K36me2_B


title: 786O_parent_sgNSD1_K36me2_A


title: 786O_ChromHMM_38E_H3K27me3_B


title: 786O cl1 SETD2resc rep 2 Input


title: RPTEC WT rep 1 Input


title: 786O_ChromHMM_38E_H3K27me2_B


title: 786O_ChromHMM_38E_H3K27Ac_B


title: 786O cl1 SETD2resc rep 1 Input


title: 786O_ChromHMM_38E_Input_B


title: 786O SETD2KO cl2 rep 2 Input


title: 786O_ChromHMM_38E_H4K4me1_B


title: 786O_ChromHMM_38E_H3K27me2_A


title: 786O_ChromHMM_38E_H4K4me1_A


title: 786O_ChromHMM_38E_H3K36me3_A


title: 786O SETD2KO cl1 rep 2 Input


title: 786O_ChromHMM_38E_H3K36me2_A


title: 786O_ChromHMM_38E_WT_Input_A


title: 786O SETD2KO cl2 rep 1 Input


title: 786O_ChromHMM_WT_H3K27me3_B


title: 786O WT rep 1 Input


title: 786O_ChromHMM_38E_H3K27Ac_A


title: 786O_ChromHMM_WT_H3K36me3_B


title: 786O_ChromHMM_38E_H3K27me3_A


title: 786O SETD2KO cl1 rep 1 Input


title: 786O_ChromHMM_WT_H3K36me2_B


title: 786O WT rep 2 Input


title: 786O_ChromHMM_WT_H3K27me2_B


title: 786O_ChromHMM_WT_H3K27Ac_B


title: 786O_ChromHMM_WT_H3K27me3_A


title: 786O_ChromHMM_WT_H3K36me3_A


title: RPTEC SETD2KO cl2 rep 2 IP


title: 786O_ChromHMM_WT_H4K4me1_B


title: RPTEC cl1 SETD2resc rep 1 IP


title: 786O_ChromHMM_WT_H3K27me2_A


title: 786O_ChromHMM_WT_H4K4me1_A


title: RPTEC SETD2KO cl2 rep 1 IP


title: RPTEC SETD2KO cl1 rep 2 IP


title: 786O_ChromHMM_WT_H3K36me2_A


title: A498_HDR_sgNSD1_Input_B


title: RPTEC SETD2KO cl1 rep 1 IP


title: A498_HDR_sgCTRL_Input_B


title: RPTEC WT rep 2 IP


title: A498_HDR_sgNSD1_Input_A


title: A498_HDR_sgNSD1_H3K36me2_B


title: RPTEC WT rep 1 IP


title: 786O cl1 SETD2resc rep 2 IP


title: 786O_ChromHMM_WT_Input_B


title: RPTEC cl1 SETD2resc rep 2 IP


title: A498_HDR_sgNSD1_H3K36me3_B


title: A498_HDR_sgCTRL_H3K36me3_B


title: A498_HDR_sgNSD1_H3K36me2_A


title: A498_HDR_sgNSD1_H3K36me3_A


title: A498_parent_sgNSD1_H3K36me3_B


title: A498_HDR_sgCTRL_H3K36me2_A


title: 786O SETD2KO cl2 rep 1 IP


title: A498_HDR_sgCTRL_H3K36me2_B


title: A498_HDR_sgCTRL_H3K36me3_A


title: 786O_ChromHMM_WT_H3K27Ac_A


title: 786O SETD2KO cl2 rep 2 IP


title: A498_parent_sgNSD1_H3K36me3_A


title: A498_parent_sgNSD1_H3K36me2_B


title: 786O_ChromHMM_WT_Input_A


title: A498_parent_sgCTRL_H3K36me3_B


title: A498_HDR_sgCTRL_Input_A


title: 786O SETD2KO cl1 rep 1 IP


title: 786O WT rep 2 IP


title: A498_parent_sgCTRL_H3K36me3_A


title: A498_parent_sgCTRL_H3K36me2_A


title: A498_parent_sgCTRL_H3K36me2_B


title: A498_parent_sgNSD1_Input_B


title: 786O cl1 SETD2resc rep 1 IP


title: A498_parent_sgNSD1_H3K36me2_A


title: A498_parent_sgNSD1_Input_A


title: HAP1-SD2-Rep2

description:
HAP1 setd2-mutant
2299-S2-Rep2_S46

data_processing:
Analysis of NGS data sets e.g. sgRNA abundance was achieved using Horizon’s data processing scripts, based on published analysis tool MAGeCK
Mean Log2-fold change in sgRNA abundance was assessed over time for each sample, with synthetic lethal hits being called based on a (LogFC delta: LocFC MUT-WT < -1.0) logic
Assembly: hg38
Supplementary files format and content: raw counts

growth_protocol: Cells were seeded in multiple 12-well plates (2x106 cells/well) in presence of 8 μg/ml Polybrene

extract_protocol:
gDNA was extracted using the QIAamp DNA Blood Maxi kit (Qiagen #51194).
Next generation sequencing of sgRNAs was carried out following PCR amplification of pooled sgRNAs to incorporate Illumina-based adaptors for 75 bp single end sequencing carried out on an Illumina sequencer

treatment_protocol: Each cell line was transduced at an MOI of 0.7 for 48 hrs, split into biological replicates, and subsequently maintained under puromycin selection (1.0 mg/mL) for the duration of the screen (12 doublings).


title: 786O WT rep 1 IP


title: A498_parent_sgCTRL_Input_B


title: LIB_Rep2

description:
HAP1 library
2299-Lib-Rep2_S70

value: Library


title: HAP1_PAR_Rep2

description:
HAP1 parental
2299-Par-Rep2_S22

value: Parental


title: LIB_Rep1

description:
HAP1 library
2299-Lib-Rep1_S58


title: 786O SETD2KO cl1 rep 2 IP


title: A498_parent_sgCTRL_Input_A


title: ALow_MD303_PBS_1 mg/kg_A-3_F3

status: Public on Jan 15 2025

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: Library name: 181692

data_processing:
Reads were aligned to the specified genome (Ensembl build 96) using STAR
Gene counts were tabulated using salmon v0.7 using default parameters (pseudoalignment mode)
Assembly: mm10, hg39
Supplementary files format and content: tab-delimited default salmon output including raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was isolated using the PureLink Pro 96 Total RNA Purification Kit (Life Technologies, Carlsbad, CA)
Tag-Seq performed using lexogen 3' QuantSeq kit FWD

value: liver

value: UTC


title: ALow_MD302_PBS_1 mg/kg_7 Days_liver_A-2_A2

description: Library name: 181452


title: ALow_MD303_PBS_1 mg/kg_A-1_F1

description: Library name: 181630


title: ALow_MD303_PBS_1 mg/kg_A-2_F2

description: Library name: 181609


title: ALow_MD302_PBS_1 mg/kg_7 Days_liver_A-4_A4

description: Library name: 181481


title: HAP1_PAR_Rep1

description:
HAP1 parental
2299-Par-Rep1_S10


title: ALow_MD303_PBS_1 mg/kg_A-4_F4

description: Library name: 181678


title: ALow_MD302_PBS_1 mg/kg_7 Days_liver_A-3_A3

description: Library name: 181456


title: ALow_MD302_PBS_1 mg/kg_7 Days_liver_A-1_A1

description: Library name: 181463


title: ACTN1_UTC_repAtx1_10.000000uM_A21_techrep1

description: Library name: 205770


title: ACTN1_UTC_repAtx1_10.000000uM_O21_techrep1

description: Library name: 205731


title: ACTN1_UTC_repAtx1_10.000000uM_I23_techrep1

description: Library name: 205816


title: ACTN1_UTC_repAtx1_10.000000uM_O23_techrep1

description: Library name: 205784


title: P15_distant

status: Public on Jan 08 2025

description:
Library name: P15_distant
sample

data_processing:
Raw reads were mapped to the GRCh38 reference genome using 10x Genomics Cell Ranger 6.0.1 to infer read counts per gene per cell
Assembly: GRCh38
Supplementary files format and content: *.mtx (count matrixes),*.tsv (barcodes, features)

source_name: distal (omentum gastric)

extract_protocol:
Tissue samples were immediately collected at the time of surgery and transferred on ice for tissue processing. Tissues were cut into small pieces and dissociated in digestion solution (1 mg/mL collagenase/Dispase [Sigma-Aldrich, cat. no. 10269638001], 1 unit/mL DNase I [NEB, cat. no. M0303], 10% fetal bovine serum (FBS) in DMEM [Sigma-Aldrich, cat. no. D8437-500mL]) for 30 min at 37°C. The omentum is a visceral adipose tissue primarily composed of adipocytes. To focus on the non-adipose cell fraction, adipocytes were separated by centrifugation and the cell pellet was collected. Red blood cell lysis (RBC) was performed using MACS red blood cell lysis solution (cat. no. 130-094-183). Subsequently, the cell pellet was resuspended into MACS dead cell removal microbeads (cat. no. 130-090-101) and was loaded into the autoMACS Pro Separator (Miltenyi Biotec, cat. no. 130-092-545)  to remove dead cells. Cells were counted and resuspended in PBS supplemented with 1% bovine serum albumin (BSA, Sigma-Aldrich, cat. no. F7524) and transferred to the Genomics Facility Basel for immediate single-cell sequencing processing. Cells were collected (350xg, 5 min), resuspended in 1 mL washing buffer consisting of PBS (Ca2+/Mg2+-free, Gibco, cat. no. 10010-015) and 1% BSA (Sigma-Aldrich, cat. no. A7906) and sequentially filtered through 100 µm (Falcon, cat. no. 352360) and 40 µm (Falcon, cat. no. 352340) cell strainers to remove cell clumps. If the cell pellet appeared still red, RBC lysis was performed following the manufacturer's instructions (Roche, cat. no. 11814389001). Apoptotic and dead cells were removed by immunomagnetic cell separation using the Annexin Dead Cell Removal Kit (StemCell Technologies, cat. no. 17899) and EasySepTM Magnet (StemCell Technologies, cat. no. 18000). Whenever required, dead cell removal was repeated to increase cell viability. Next, cells were washed with a resuspension buffer (PBS with 0.05% BSA), spun down and resuspended in a resuspension buffer. Cell numbers and viability were assessed at each step on a Cellometer K2 Image Cytometer (Nexcelom Bioscience, cat. no. Cellometer K2) using ViaStain AOPI Staining Solution (Nexcelom Bioscience, cat. no. CS2-0106-5mL) and PD100 cell counting slides (Nexcelom Bioscience, cat. no. CHT4-PD100-003). Fresh sample processing resulted in overall high sample quality with an average 88.3% cell viability (final count before droplet encapsulation and scRNA-seq processing
10x Genomics Chromium platform with the Next GEM Single Cell 3’ Reagent Kit v3.1 on 10x Genomics Chromium Single Cell Controller

value: distal (omentum gastric)


title: ACTN1_UTC_repAtx1_10.000000uM_M21_techrep1

description: Library name: 205800


title: P15_tumor

description:
Library name: P15_tumor
sample

source_name: tumor (omentum majus)

value: tumor (omentum majus)


title: ACTN1_UTC_repAtx1_10.000000uM_G21_techrep1

description: Library name: 205729


title: HAP1-SD2-Rep1

description:
HAP1 setd2-mutant
2299-S2-Rep1_S34


title: P14_distant

description:
Library name: P14_distant
sample

source_name: distal (omentum minus)

value: distal (omentum minus)


title: P14_peritumoral

description:
Library name: P14_peritumoral
sample

source_name: peritumoral (omentum majus)

value: peritumoral (omentum majus)


title: P15_peritumoral

description:
Library name: P15_peritumoral
sample


title: P13_distant

description:
Library name: P13_distant
sample


title: P13_peritumoral

description:
Library name: P13_peritumoral
sample


title: P13_tumor

description:
Library name: P13_tumor
sample


title: P12_distant

description:
Library name: P12_distant
sample


title: P12_peritumoral

description:
Library name: P12_peritumoral
sample


title: P10_distant

description:
Library name: P10_distant
sample


title: P10_peritumoral

description:
Library name: P10_peritumoral
sample


title: P10_tumor

description:
Library name: P10_tumor
sample


title: P7_proximal

description:
Library name: P7_proximal
sample

source_name: omentum majus

value: omentum majus


title: P9_tumor

description:
Library name: P9_tumor
sample


title: P6_distal

description:
Library name: P6_distal
sample

source_name: omentum minus

value: omentum minus


title: P11_peritumoral

description:
Library name: P11_peritumoral
sample


title: P9_distant

description:
Library name: P9_distant
sample


title: P8_proximal

description:
Library name: P8_proximal
sample


title: P6_lesser_omentum

description:
Library name: P6_lesser_omentum
sample

source_name: omentum gastric

value: omentum gastric


title: P9_peritumoral

description:
Library name: P9_peritumoral
sample


title: P6_proximal

description:
Library name: P6_proximal
sample


title: P5_distal

description:
Library name: P5_distal
sample


title: P5_proximal

description:
Library name: P5_proximal
sample


title: P14_tumor

description:
Library name: P14_tumor
sample


title: P1_proximal

description:
Library name: P1_proximal
sample


title: P3_lesser_omentum

description:
Library name: P3_lesser_omentum
sample


title: P4_proximal

description:
Library name: P4_proximal
sample


title: P3_distal

description:
Library name: P3_distal
sample


title: P4_distal

description:
Library name: P4_distal
sample


title: AGY594_T60NaCl_R2

status: Public on Jan 03 2025

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description:
Library name: Gasch1455
Gasch1455

data_processing:
Trimmed reads with Trimmomatic 0.39
Reading mapping to S288c genome using Bowtie 2 version 2.4.4
Read counts calculated with HTSeq-count version 0.6.0
Assembly: default yeast reference, SGD R64-1-1 equivalent to UCSC sacCer3
Supplementary files format and content: raw HTSeq counts

organism: Saccharomyces cerevisiae BY4741

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were grown in low fluorescence media in shake flasks to mid log phase in batch cultures in shaker flasks at 30C.

extract_protocol:
Total RNA was extracted using hot phenol lysis and purified using the RNeasy MinElute Cleanup Kit (QIAGEN, Hilden, Germany). rRNA depletion was performed with the EPiCenter Ribo-Zero Magnetic Gold Kit (Yeast) RevA kit (Illumina Inc, San Diego, CA).
RNA-seq libraries were prepared using a TruSeq Stranded Total RNA kit (Illumina), and PCR purified using AMPure XP beads (Beckman Coulter, Indianapolis, IN).

treatment_protocol: Sodium chloride was added to 0.7M final concentration and cells were collected at 10, 20, 30, 40, 50, 60, and 90 min after treatment.

value: Saccharomyces cerevisiae

tag: strain

value: dot6 tod6 deletion

tag: media

value: low fluorescence media

tag: stress

value: 60 minutes post NaCl stress


title: P2_distal

description:
Library name: P2_distal
sample

tag: batch


title: P2_proximal

description:
Library name: P2_proximal
sample


title: P3_proximal

description:
Library name: P3_proximal
sample


title: P2_lesser_omentum

description:
Library name: P2_lesser_omentum
sample


title: P4_lesser_omentum

description:
Library name: P4_lesser_omentum
sample


title: AGY594_T90NaCl_R2

description:
Library name: Gasch1459
Gasch1459

value: 90 minutes post NaCl stress


title: AGY594_T40NaCl_R2

description:
Library name: Gasch1447
Gasch1447

value: 40 minutes post NaCl stress


title: AGY594_T30NaCl_R2

description:
Library name: Gasch1443
Gasch1443

value: 30 minutes post NaCl stress


title: AGY594_T0NaCl_R2

description:
Library name: Gasch1431
Gasch1431

value: unstressed


title: AGY2046_T90NaCl_R2

description:
Library name: Gasch1458
Gasch1458

value: msn2 msn4 deletion


title: AGY594_T10NaCl_R2

description:
Library name: Gasch1435
Gasch1435

value: 10 minutes post NaCl stress


title: AGY2046_T50NaCl_R2

description:
Library name: Gasch1450
Gasch1450

value: 50 minutes post NaCl stress


title: AGY594_T20NaCl_R2

description:
Library name: Gasch1439
Gasch1439

value: 20 minutes post NaCl stress


title: AGY594_T50NaCl_R2

description:
Library name: Gasch1451
Gasch1451


title: AGY2046_T20NaCl_R2

description:
Library name: Gasch1438
Gasch1438


title: AGY2046_T60NaCl_R2

description:
Library name: Gasch1454
Gasch1454


title: AGY2046_T0NaCl_R2

description:
Library name: Gasch1430
Gasch1430


title: AGY2046_T10NaCl_R2

description:
Library name: Gasch1434
Gasch1434


title: AGY2046_T30NaCl_R2

description:
Library name: Gasch1442
Gasch1442


title: AGY4_T60NaCl_R2

description:
Library name: Gasch1453
Gasch1453

value: wild-type


title: AGY4_T90NaCl_R2

description:
Library name: Gasch1457
Gasch1457


title: AGY2046_T40NaCl_R2

description:
Library name: Gasch1446
Gasch1446


title: P12_tumor

description:
Library name: P12_tumor
sample

value: tumor (omentum majus)


title: AGY4_T50NaCl_R2

description:
Library name: Gasch1449
Gasch1449


title: AGY4_T30NaCl_R2

description:
Library name: Gasch1441
Gasch1441


title: AGY4_T10NaCl_R2

description:
Library name: Gasch1433
Gasch1433


title: AGY4_T40NaCl_R2

description:
Library name: Gasch1445
Gasch1445


title: AGY594_T60NaCl_R1

description:
Library name: Gasch1419
Gasch1419


title: AGY4_T20NaCl_R2

description:
Library name: Gasch1437
Gasch1437


title: AGY594_T90NaCl_R1

description:
Library name: Gasch1423
Gasch1423


title: AGY4_T0NaCl_R2

description:
Library name: Gasch1429
Gasch1429


title: AGY594_T20NaCl_R1

description:
Library name: Gasch1403
Gasch1403


title: AGY594_T10NaCl_R1

description:
Library name: Gasch1399
Gasch1399


title: AGY594_T40NaCl_R1

description:
Library name: Gasch1411
Gasch1411


title: AGY2046_T90NaCl_R1

description:
Library name: Gasch1422
Gasch1422


title: AGY594_T30NaCl_R1

description:
Library name: Gasch1407
Gasch1407


title: AGY2046_T50NaCl_R1

description:
Library name: Gasch1414
Gasch1414


title: AGY2046_T30NaCl_R1

description:
Library name: Gasch1406
Gasch1406


title: AGY2046_T60NaCl_R1

description:
Library name: Gasch1418
Gasch1418


title: AGY2046_T40NaCl_R1

description:
Library name: Gasch1410
Gasch1410


title: AGY2046_T10NaCl_R1

description:
Library name: Gasch1398
Gasch1398


title: AGY4_T90NaCl_R1

description:
Library name: Gasch1421
Gasch1421


title: AGY2046_T0NaCl_R1

description:
Library name: Gasch1394
Gasch1394


title: AGY4_T50NaCl_R1

description:
Library name: Gasch1413
Gasch1413


title: AGY4_T20NaCl_R1

description:
Library name: Gasch1401
Gasch1401


title: AGY2046_T20NaCl_R1

description:
Library name: Gasch1402
Gasch1402


title: AGY4_T0NaCl_R1

description:
Library name: Gasch1393
Gasch1393


title: AGY4_T30NaCl_R1

description:
Library name: Gasch1405
Gasch1405


title: AGY594_T50NaCl_R1

description:
Library name: Gasch1415
Gasch1415


title: UIRI+Nx d7_6

status: Public on Dec 31 2024

city: Aachen

first: Benjamin

middle: Arthur

last: Vervaet

address: Pauwelstrasse 30

country: Germany

institute: RWTH Uniklinik Aachen

description: CCA-01 69

data_processing:
Trimmomatic was used to remove the leading and trailing 20 bases from reads, ensure a minimum quality score of 20 over a sliding window of 4 bases, remove Illumina-specific adapter sequences (barcodes) and ensure a minimum read length of 36 bases.
Sequences were mapped against the Ensembl release 86 reference mouse genome (GRCm38) using STAR
HTseq (v0.6.1) was used to count all reads for each gene and set up a read count table.
Assembly: mm10
Supplementary files format and content: tab delimited tekst file includes all raw counts for each sample

source_name: Kidney

extract_protocol:
Total mRNA was extracted from a cryo pole section of the kidney using the PureLink® RNA Mini kit from Invitrogen
Libraries for RNA were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH). Input of 500 ng of total mRNA was used.

value: Kidney


title: UIRI+Nx d7_5

description: CCA-01 68


title: UIRI d3_4

description: CCA-01 58


title: UIRI+Nx d7_4

description: CCA-01 44


title: AGY594_T0NaCl_R1

description:
Library name: Gasch1395
Gasch1395


title: Control_5

description: CCA-01 63


title: UIRI d3_5

description: CCA-01 65


title: Control_6

description: CCA-01 64


title: UIRI d3_6

description: CCA-01 66


title: UIRI+Nx d7_1

description: CCA-01 08


title: UIRI d7_6

description: CCA-01 57


title: UIRI d7_1

description: CCA-01 43


title: AGY4_T60NaCl_R1

description:
Library name: Gasch1417
Gasch1417


title: UIRI d7_3

description: CCA-01 54


title: UIRI d7_2

description: CCA-01 45


title: UIRI d7_5

description: CCA-01 56


title: UIRI d7_4

description: CCA-01 55


title: AGY4_T10NaCl_R1

description:
Library name: Gasch1397
Gasch1397


title: UIRI d3_1

description: CCA-01 51


title: AGY4_T40NaCl_R1

description:
Library name: Gasch1409
Gasch1409


title: Control_1

description: CCA-01 47


title: Control_4

description: CCA-01 50


title: Control_2

description: CCA-01 48


title: Control_3

description: CCA-01 49


title: PBMC_scRNAseq_LL_12

status: Public on Dec 18 2024

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

data_processing:
Cell Ranger (10x Genomics, v6.0.1) was used to performalignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: Peripheral blood mononuclear cells

extract_protocol:
fasting blood was collected into Vacutainer tubes containing anticoagulant citrate dextrose solution A (BD, 364606). Briefly, whole blood was processed within 2h of receipt and centrifuged at 480 g for 10 min. at room temperature (RT). Plasma was collected and the cell fraction diluted 1:2 in PBS, then placed in Ficoll-Paque PLUS density gradient media (GE Healthcare Life Sciences, 17144003) and centrifuged at 1,250 g for 20 min. at RT. The PBMC layer was collected, washed twice in PBS and resuspended at 2–5×105 cells per ml in 50% vol/vol RPMI-1640 (Gibco, 11875093) 40% vol/vol FBS 10% dimethyl sulfoxide (Tocris Bioscience, 3176) for frozen storage at –80 °C or liquid N2. On experiment date, specimens were thawed, washed and their viability assessed using a Cellometer Auto 2000 (Nexcellom).
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively) according to the manufacturer’s instructions.

value: Peripheral blood mononuclear cells

tag: condition

value: CONTROL

value: followup


title: PBMC_scRNAseq_NT_12

value: baseline


title: UIRI+Nx d7_2

description: CCA-01 09


title: UIRI+Nx d7_3

description: CCA-01 42


title: PBMC_scRNAseq_LL_11


title: PBMC_scRNAseq_LL_8


title: PBMC_scRNAseq_NT_11


title: PBMC_scRNAseq_LL_7


title: PBMC_scRNAseq_NT_9


title: PBMC_scRNAseq_LL_9


title: PBMC_scRNAseq_NT_7


title: UIRI d3_3

description: CCA-01 59


title: PBMC_scRNAseq_NT_8


title: PBMC_scRNAseq_NT_4


title: PBMC_scRNAseq_NT_5


title: PBMC_scRNAseq_LL_6


title: PBMC_scRNAseq_NT_3


title: PBMC_scRNAseq_NT_6


title: UIRI d3_2

description: CCA-01 52


title: PBMC_scRNAseq_LL_5


title: PBMC_scRNAseq_NT_2


title: PBMC_scRNAseq_LL_3


title: PBMC_scRNAseq_LL_2


title: 16_P-40_TIL (scRNA-seq)

status: Public on Dec 16 2024

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description:
barcode number 16
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

data_processing:
Read alignment and counting was conducted using 10x Genomics CellRanger (v6.1.1).
Assembly: hg38
Supplementary files format and content: 10x genomics CellRanger aggregated expression matrix output (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
Supplementary files format and content: 10x genomics CellRanger VDJ contigs

source_name: tumor

extract_protocol:
Fresh tumors were mechanically disruped, resuspended in RPMI media, strained by 70 um strainer, and percoll seperated to enrich for leukocytes. Single cell suspensions were cryopreserved in liquid nitrogen and thawed at 37C for sequencing.
Chromium single cell controller generated droplet emulsion of single-cells and barcoded gel beads. RNA seq libraries were generated using the single cell 5’ DGE Library and Gel Bead Kit v3.1 (10x Genomics). Single cell TCR seq libraries were generated with the Single Cell V(D)J Enrichment Kit ( Human T Cell) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics). The libraries for digital gene expression were sequenced using NovaSeq 6000 system (Illumina).

treatment_protocol: Patients received priming doses of neoadjuvant cancer immunotherapy prior to surgical resection of their primary tumor. Treatments consisted of cyclophosphamide (Cy)/GVAX vaccine (Arm A), Cy/GVAX and anti-PD1 (nivolumab, Arm B), or Cy/GVAX, anti-PD1, and CD137 agonist (urelumab, a human IgG4 agonistic monoclonal antibody, Arm C).

value: tumor


title: 8_P-23_TIL (scRNA-seq)

description:
barcode number 8
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 15_P-46_TIL (scRNA-seq)

description:
barcode number 15
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: PBMC_scRNAseq_LL_1


title: PBMC_scRNAseq_NT_1


title: PBMC_scRNAseq_LL_10


title: 7_P-25_TIL (scRNA-seq)

description:
barcode number 7
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 6_P-3_TIL (scRNA-seq)

description:
barcode number 6
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 2_P-17_TIL (scRNA-seq)

description:
barcode number 2
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: PBMC_scRNAseq_NT_10


title: 10_P-32_TIL (scRNA-seq)

description:
barcode number 10
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 5_P-33_TIL (scRNA-seq)

description:
barcode number 5
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 1_P-24_TIL (scRNA-seq)

description:
barcode number 1
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 3_P-6_TIL (scRNA-seq)

description:
barcode number 3
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 13_P-42_TIL (scRNA-seq)

description:
barcode number 13
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 12_P-2_TIL (scRNA-seq)

description:
barcode number 12
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: 11_P-44_TIL (scRNA-seq)

description:
barcode number 11
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: PBMC_scRNAseq_LL_4


title: 15_P-46_TIL (scTCR-seq)

description: barcode number 15


title: 2_P-17_TIL (scTCR-seq)

description: barcode number 2


title: 14_P-45_TIL (scRNA-seq)

description: barcode number 14


title: 8_P-23_TIL (scTCR-seq)

description: barcode number 8


title: 10_P-32_TIL (scTCR-seq)

description: barcode number 10


title: 16_P-40_TIL (scTCR-seq)

description: barcode number 16


title: 7_P-25_TIL (scTCR-seq)

description: barcode number 7


title: 6_P-3_TIL (scTCR-seq)

description: barcode number 6


title: 1_P-24_TIL (scTCR-seq)

description: barcode number 1


title: 5_P-33_TIL (scTCR-seq)

description: barcode number 5


title: 3_P-6_TIL (scTCR-seq)

description: barcode number 3


title: 12_P-2_TIL (scTCR-seq)

description: barcode number 12


title: 13_P-42_TIL (scTCR-seq)

description: barcode number 13


title: 11_P-44_TIL (scTCR-seq)

description: barcode number 11


title: 4_P-20_TIL (scRNA-seq)

description:
barcode number 4
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz