title: Sorted nuclei, muscle

city: Bethesda

first: Elisabeth

last: Heuston

state: MD

address: 50 South Drive, Bldg 50, Rm 5531

department: National Human Genome Research Institute

institute: NIH/NHGRI

description: 10X Genomics 5' GEX

data_processing:
Demultiplexing was done in Cell Ranger_7.2.0 (10x Genomics) and mapped to the GRCh38-2020-A transcriptome. Ambient RNA excluded with CellBender_0.3.0 21.
Assembly: GRCh38-2020-A
Supplementary files format and content: Following CellBender_0.3.0 ambient RNA removal, files were exported as X-cb-seurat_feature_bc_matrix_filtered.h5 files.

source_name: Skeletal muscle

extract_protocol:
Skeletal muscle samples were obtained from the vastus lateralis muscle under local anesthesia and issected into visible skeletal muscle and adipose tissue components, and each component was immediately placed in a tube and prefilled with at least 5 ml of Allprotect® Tissue Reagent. Preserved skeletal muscle specimens stored in ATR were thawed on ice. Ice cold PBS was added and pipette-mixed with ATR to dilute and remove supernatant. This process was repeated until all ATR was removed. Tissue was subsequently rinsed twice in ice cold PBS to remove any remaining ATR, weighed, and resuspended in pBSA (PBS + 0.04% BSA) + 1U/mL RNaseOut (RNaseOUT™ Recombinant RNase Inhibitor, Thermo Fisher Scientific, Waltham, MA, catalogue no. 10777019). Manual tissue dissociation was performed with a disposable micro-tissue homogenizer. Cell concentrations were estimated with a hemocytometer. Single cell suspensions were strained sequentially through 70 µm and 40 µm filters, with washes between each step. For sorted samples, cells were stained with a final concentration of 25 µg/mL anti-Nuclear Pore Complex conjugated to Alexa Fluor® 594 (NPC-AF594) antibody (BioLegend, San Diego, CA, catalogue no. 682202) and NPC+ cells isolated on a Becton Dickinson FACS ARIA Fusion using a 70 µm nozzle. For nuclei isolation, cells were incubated with Nuclear Extraction Buffer (Miltenyi Biotec, Gaithersburg, MD, catalogue no. 130-128-024) containing 1 U/mL RNaseOut at 4˚C for 5 minutes. Following the incubation, suspensions were centrifuged at 300 x g, 4°C, 5 minutes, supernatant removed, and nuclei resuspended in pBSA. Samples were sorted on ice into pBSA before downstream processing. Note that “sorted nuclei” refers to cells that were sorted prior to nuclei extraction.
Libraries were prepared using a Chromium Single Cell 5’ Library & Gel Bead Kit v2 (P/N 1000263, 10x Genomics). GEM-RT was performed in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad; P/N 1851197). Following retrotranscription, GEMs were broken and the single-strand cDNA was purified with DynaBeads MyOne Silane Beads. cDNA was amplified using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module:. Amplified cDNA product was purified with the SPRIselect Reagent Kit (0.6× SPRI). Indexed sequencing libraries were constructed using the reagents in the Chromium Single Library construction kit, following these steps: (1) end repair and A-tailing; (2) adaptor ligation; (3) post-fragmentation, end repair, and A-tailing double size selection cleanup with SPRI-select beads; (4) sample index PCR and cleanup. The barcoded sequencing libraries were diluted at 3 nM and sequenced on Illumina NovaSeqX.

value: Skeletal muscle

value: Sorted nuclei


title: Rice, 5 days after sowing, replicate 1

status: Public on Nov 21 2024

type: SRA

city: Canberra

first: Florence

middle: R

last: Danila

state: ACT

address: Building 134 Linneaus Way, Acton

country: Australia

institute: Australian National University

description: sequenced thru BGI HongKong using DNBseq platform

library_source: transcriptomic

data_processing:
Raw reads were trimmed for adapter sequences, unknown bases, and low-quality base-calls, before being mapped to the corresponding reference genomes (IRGSP-1.0-Oryza_sativa; Setaria viridis v2) using Bowtie2 (Langmead and Salzberg 2012).
Expression quantification was performed using RSEM (Li and Dewey, 2011) on transcripts defined in the corresponding reference annotations (Oryza_sativa.IRGSP-1.0.51.gff3, Setaria_viridis_v2.0.51.gff3). Genes detected at CPM > 1 in at least four samples were retained for analysis.
Fold-changes in expression were estimated with DEseq2 (Li and Dewey 2011; Love et al. 2014).
Assembly: IRGSP-1.0-Oryza_sativa; Setaria viridis v2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log2fold change and gene details for each sample

molecule: polyA RNA

organism: Oryza sativa

source_name: Leaf

growth_protocol: Seeds from homozygous ZmPDLP1-YFP rice and setaria lines were surface sterilized and sown in Murashige and Skoog medium supplemented with 30 g sucrose/L in magenta boxes. Both species were grown in a controlled growth cabinet maintained at 14-h photoperiod, 28°C/24°C day/night temperatures, 60% relative humidity, and ambient CO2 concentration.

extract_protocol:
Total RNA was extracted using the Plant RNeasy kit (Qiagen) as per the manufacturer's instructions.
Poly(A)-enriched RNA sequencing (mRNA sequencing) libraries were constructed and sequenced (100 bp paired-end with 30M clean reads per sample) on a DNBSEQ (DNBSEQ Technology, MGI Co. Ltd.) platform by BGI Genomics (Hong Kong).

treatment_protocol: Leaf tissue samples taken at 1, 3, 5, 7, 9 and 18 days after sowing (DAS) from 30 individual plants for each of the 3-4 biological replicates were flash frozen in liquid nitrogen and stored at -80°C for RNA isolation.

tag: tissue

value: Leaf

tag: ecotype

value: Kitaake

tag: genotype

tag: developmental stage

value: 5 days after sowing


title: Rice, 3 days after sowing, replicate 2

value: 3 days after sowing


title: Rice, 3 days after sowing, replicate 4


title: A549, C36, 24 h, rep1

city: Columbia

first: Donald

last: Burke-Agüero

state: Missouri

address: 1201 Rollins St

department: molecular microbiology and immunology

country: USA

institute: University of Missouri

data_processing:
Trimmed fastq files were mapped to the reference genome GRCh38.p12 using hisat2
Cufflink was used to calculate the FPKM
Cuffdiff was used to identify the differentially expressed genes
Assembly: hg38
Supplementary files format and content: comma-seperated text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: RPMI (H1975, H820, H3255) or DMEM (A549) supplemented  10% (maintence) or 1% (treatment) Fetal Bovine Serum, 1 mM sodium pyruvate, 2 mM L-glutamine, and 1X NEAAs.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit (NEB) according to manfacuters protocol. RNA concentration and purity was assessed using a NanoDrop (ThermoFisher). RNA was stored at -80C until submission for NGS.
Libraries were constructed using the Illumina Stranded mRNA Prep following the manufactures protocol. This is a poly-A enrichment approach. Unique dual-indexes were used to barcode libraries.
RNA-Seq; Sequences were generated on a NovaSeq 6000 using a paired end, 100 base read length run. Files were provided in FASTQ format.

treatment_protocol: Aptamers were folded at 10X in 1X DPBS + 5mM MgCl2. Aptamers were diluted to 1X in media and added to cells for 24 h before RNA extraction.

tag: cell line

tag: cell type

value: NSCLC cell line

value: WT EGFR

tag: treatment


title: Filtered nuclei, muscle

description: 10X Genomics 5' GEX

library_source: transcriptomic single cell

tag: group

value: Filtered nuclei


title: Filtered cells, muscle

description: 10X Genomics 5' GEX

value: Filtered cells


title: Female_Unwounded_Skin_1

type: RNA

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

hyb_protocol: Xenium in situ analysis

scan_protocol: Xenium in situ analysis

data_processing: Slides were processed and segmented with Xenium Onboard Analyzer v1.6.1 software and analyzed with Xenium Explorer v2.0.0 software.

organism: Mus musculus

source_name: Dorsal skin, healthy

label_protocol: Sections on Xenium slides (10X Genomics) were processed with the Xenium In Situ Gene Expression Kit (10X Genomics).

extract_protocol: 5µm Formalin-fixed paraffin embedded sections were cut directly onto four separated Xenium slides under RNAse-free conditions: 1) Unwounded Control and PITX1+ male dorsal skin. 2) Unwounded Control and PITX1+ female dorsal skin. 3) Unwounded male and female buccal mucosa. 4) POD4 wounded Control and PITX1+ male dorsal skin.

value: Dorsal skin

value: Control & PITX1+

value: Vehicle & Doxycycline


title: Rice, 3 days after sowing, replicate 1


title: Human bronchial epithelial cells, 48hr, MCC, replicate 3

status: Public on Nov 20 2024

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description:
Gene expression after 48hr in MCC-exposed Human bronchial epithelial cells
CF040_09

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Human Genome Microarray (G2519F-014850; Agilent Technologies) at 65 °C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent) at 5 μm resolution.

data_processing:
The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.
log2 average normalized signal intensity

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Human bronchial epithelial cells (BEAS-2B), obtained from the American Type Culture Collection (ATCC® CRL-9609™), were cultured at 37 °C in 6-well plates using BEGM (Lonza, Basel, Switzerland) in a humidified atmosphere of 95% air and 5% CO₂.

extract_protocol: Total RNA was extracted using QIAzol Lysis Reagent (Qiagen, Japan) following the manufacturer’s instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., US), and sample qualities were monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, US).

treatment_protocol: The BEGM was removed, and the cells were treated with working solutions of eight types of CNFs (CNF1, CNF2, CNF3, CNF4, CNF5, CNF6, CNF7, or CNF8) as well as MCC. At this point, the cells were approximately 40% confluent. Then incubated for 48 hours at 37 °C in a humidified incubator with 5% CO₂.

tag: cell

value: MCC

tag: time


title: Human bronchial epithelial cells, 48hr, MCC, replicate 2

value: Human bronchial epithelial cells (BEAS-2B)


title: Human bronchial epithelial cells, 48hr, CNF8, replicate 1

description:
Gene expression after 48hr in CNF8-exposed Human bronchial epithelial cells
CF040_08


title: Human bronchial epithelial cells, 48hr, MCC, replicate 1


title: Male_Unwounded_Skin_1


title: Human bronchial epithelial cells, 48hr, CNF8, replicate 2


title: Human bronchial epithelial cells, 48hr, MCC, replicate 4


title: Human bronchial epithelial cells, 48hr, CNF7, replicate 3

description:
Gene expression after 48hr in CNF7-exposed Human bronchial epithelial cells
CF040_07


title: Male_Wounded_Skin_1

source_name: POD4 wounded dorsal skin

value: POD4 wounded dorsal skin


title: Human bronchial epithelial cells, 48hr, CNF8, replicate 4


title: Human bronchial epithelial cells, 48hr, CNF8, replicate 3


title: MU2AF1-S34F, scRNA-seq

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
For scRNA-seq, read alignment and expression matrice generation were done via cellranger. For bulk RNA-seq, read alignment were done using STAR.
Seurat was used to analyze the single cell datasets. DESeq2 was used to analyze the bulk RNA-seq data.
Assembly: hg38
Supplementary files format and content: raw expression counts

source_name: primary cells

growth_protocol: BMMNCs were enriched in CD34+ cells using magnetic separation with the CD34 Microbead Kit (Miltenyi Biotec), and Enriched CD34+ cells were precultured in stem cell expansion medium (StemSpan SFEM II, StemCell Technologies) supplemented with 1% penicillin/streptomycin-glutamine (Gibco) and hematopoietic cytokines (100 ng/ml SCF, 100 ng/ml FLT3L, and 100 ng/ml TPO; Peprotech) at 37°C in a 5% CO2 incubator for 24 hours prior transduction. The pRCDCMEGP-CMV-U2AF1S34-EF1-TagGFP2-2A-Puro or the pRCDCMEGP-CMV-U2AF1wild-type-EF1-TagGFP2-2A-Puro vectors, expressing the U2AF1S34 or the U2AF1wild-type allele, respectively.

extract_protocol:
live GFP+ CD34+ cells were sorted by flow cytometry and submitted for sequening
For single cell RNA 3’ sequencing, Sorted transduced CD34+ cell concentration and viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (catalog number #PN120236, 10x Genomics), and single cells were lysed and barcoded for reverse transcription, as previously described.9 Briefly, libraries were sequenced using the NovaSeq6000 SP 100-cycle flow cell (Illumina). Sequencing analysis was performed using the 10x Genomics’ Cell Ranger software.   For single cell 5’ sequencing, Sorted CD34+ cells from NIH-39 were processed for 5’ scRNA-seq library preparation using Chromium Next GEM Single Cell 5’ kit v2 (10x Genomics, catalog number #PN-1000265). Libraries were sequenced on the Illumina NovaSeq 6000 system. Single cell expression measurements (digital counts) were obtained from raw sequence data (FASTQ) with the 10x Genomics Cell Ranger pipeline v4.0.0 (default settings, the GRCh38 reference).  For bulk RNA sequencing, Total RNA from sorted U2AF1S34 or U2AF1wild-type transduced CD34+ cells was purified using the PicoPure RNA Isolation Kit (catalog number #KIT0204, ThermoFisher Scientific). Quality checks and quantifications were performed with the 2100 Expert Bioanalyzer (Agilent). Illumina low input total RNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (catalog number #634412; Takara Bio), as previously described.15 Libraries were combined and sequenced on the Illumina NextSeq500 sequencer using the High Output 150 cycle flow cell with the 100nt PE format.

tag: disease

value: No

value: TERT mutation

value: BM CD34+

value: primary cells

tag: conditions

value: overexpressed U2AF1 S34F

value: No treatment


title: Human bronchial epithelial cells, 48hr, CNF6, replicate 4

description:
Gene expression after 48hr in CNF6-exposed Human bronchial epithelial cells
CF040_06


title: Human bronchial epithelial cells, 48hr, CNF7, replicate 1


title: Human bronchial epithelial cells, 48hr, CNF6, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF6, replicate 3


title: Sorted cells, muscle

description: 10X Genomics 5' GEX

value: Skeletal muscle

value: Sorted cells


title: Buccal_Mucosa

source_name: Buccal mucosa, healthy

value: Buccal mucosa

value: Control

value: Vehicle


title: Rice, 3 days after sowing, replicate 3

value: Leaf

value: Kitaake

value: 3 days after sowing


title: Human bronchial epithelial cells, 48hr, CNF6, replicate 1


title: Human bronchial epithelial cells, 48hr, CNF5, replicate 4

description:
Gene expression after 48hr in CNF5-exposed Human bronchial epithelial cells
CF040_05


title: Human bronchial epithelial cells, 48hr, CNF5, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF5, replicate 1


title: Human bronchial epithelial cells, 48hr, CNF4, replicate 4

description:
Gene expression after 48hr in CNF4-exposed Human bronchial epithelial cells
CF040_04


title: Human bronchial epithelial cells, 48hr, CNF5, replicate 3


title: Human bronchial epithelial cells, 48hr, CNF7, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF7, replicate 4


title: Human bronchial epithelial cells, 48hr, CNF4, replicate 1


title: Human bronchial epithelial cells, 48hr, CNF4, replicate 3


title: Human bronchial epithelial cells, 48hr, CNF3, replicate 1

description:
Gene expression after 48hr in CNF3-exposed Human bronchial epithelial cells
CF040_03


title: Human bronchial epithelial cells, 48hr, CNF4, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF3, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF2, replicate 3

description:
Gene expression after 48hr in CNF2-exposed Human bronchial epithelial cells
CF040_02


title: Human bronchial epithelial cells, 48hr, CNF3, replicate 3


title: Human bronchial epithelial cells, 48hr, CNF3, replicate 4


title: Human bronchial epithelial cells, 48hr, CNF2, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF2, replicate 1


title: Human bronchial epithelial cells, 48hr, CNF1, replicate 1

description:
Gene expression after 48hr in CNF1-exposed Human bronchial epithelial cells
CF040_01


title: Human bronchial epithelial cells, 48hr, CNF1, replicate 2


title: Human bronchial epithelial cells, 48hr, CNF1, replicate 4


title: Human bronchial epithelial cells, 48hr, CNF1, replicate 3


title: Human bronchial epithelial cells, 48hr, Control for CNF7, CNF8, and MCC, replicate 4

description:
Gene expression after 48hr in Human bronchial epithelial cells as vehicle cotrol
CF040_C4

value: Vehicle control for CNF7, CNF8 and MCC


title: Human bronchial epithelial cells, 48hr, Control for CNF7, CNF8, and MCC, replicate 3

value: Human bronchial epithelial cells (BEAS-2B)


title: Human bronchial epithelial cells, 48hr, CNF2, replicate 4


title: Human bronchial epithelial cells, 48hr, Control for CNF7, CNF8, and MCC, replicate 1


title: Human bronchial epithelial cells, 48hr, Control for CNF7, CNF8, and MCC, replicate 2


title: Human bronchial epithelial cells, 48hr, Control for CNF5 and CNF6, replicate 2

description:
Gene expression after 48hr in Human bronchial epithelial cells as vehicle cotrol
CF040_C3

value: Vehicle control for CNF5 and CNF6


title: Human bronchial epithelial cells, 48hr, Control for CNF5 and CNF6, replicate 4


title: Human bronchial epithelial cells, 48hr, Control for CNF2 and CNF4, replicate 4

description:
Gene expression after 48hr in Human bronchial epithelial cells as vehicle cotrol
CF040_C2

value: Vehicle control for CNF2 and CNF4


title: Human bronchial epithelial cells, 48hr, Control for CNF5 and CNF6, replicate 3


title: Human bronchial epithelial cells, 48hr, Control for CNF2 and CNF4, replicate 3


title: Human bronchial epithelial cells, 48hr, Control for CNF5 and CNF6, replicate 1


title: Human bronchial epithelial cells, 48hr, Control for CNF2 and CNF4, replicate 1


title: Human bronchial epithelial cells, 48hr, Control for CNF1 and CNF3, replicate 4

description:
Gene expression after 48hr in Human bronchial epithelial cells as vehicle cotrol
CF040_C1

value: Vehicle control for CNF1 and CNF3


title: Human bronchial epithelial cells, 48hr, Control for CNF2 and CNF4, replicate 2


title: Human bronchial epithelial cells, 48hr, Control for CNF1 and CNF3, replicate 3


title: Human bronchial epithelial cells, 48hr, Control for CNF1 and CNF3, replicate 2


title: Human bronchial epithelial cells, 48hr, Control for CNF1 and CNF3, replicate 1


title: ICC_JFE_HS_352NT

city: Villejuif

first: Sylvie

last: JOB

address: UMR-S 1193 INSERM/Université Paris Saclay Hôpital Paul Brousse

country: France

institute: INSERM

description: Gene expression data from normal tissue

hyb_protocol: Following fragmentation and end-labeling, 4.7 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Human Transcriptome Array 2.0 (Affymetrix).

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.3.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene level.

label: biotin

source_name: Normal

label_protocol: Biotinylated double strand cDNA targets were prepared, starting from 1 to 20 ng of total RNA with the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: Total RNA was extracted using the mirVana miRNA isolation kit (Thermo Fisher Scientific, France).

treatment_protocol: Each frozen specimen was cut at 5μm and stained with hematein-eosin-saffron at two opposite ends and analyzed by an expert in liver pathology (CG) to evaluate semi-quantitatively the proportion of cancer cells, the degree of necrosis and fibrosis, and the percent cellularity.

value: Normal

tag: Sex

value: F

tag: age

tag: tnm


title: ICC_JFE_HS_336NT

description: Gene expression data from normal tissue

value: M


title: ICC_JFE_HS_338NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_376NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_313NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_365NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_399NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_401NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_331NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_370NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_303T

description: Gene expression data from HCC

source_name: HCC

value: HCC tumor


title: ICC_JFE_HS_304T

description: Gene expression data from HCC


title: ICC_JFE_HS_319T

description: Gene expression data from HCC


title: ICC_JFE_HS_317T

description: Gene expression data from HCC


title: ICC_JFE_HS_322T

description: Gene expression data from HCC


title: ICC_JFE_HS_310T

description: Gene expression data from HCC


title: ICC_JFE_HS_346NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_318T

description: Gene expression data from HCC


title: ICC_JFE_HS_313T

description: Gene expression data from HCC


title: ICC_JFE_HS_403NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_405NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_314T

description: Gene expression data from HCC


title: ICC_JFE_HS_345NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_315T

description: Gene expression data from HCC


title: ICC_JFE_HS_409NT

description: Gene expression data from normal tissue


title: ICC_JFE_HS_305T

description: Gene expression data from HCC


title: ICC_JFE_HS_324T

description: Gene expression data from HCC


title: ICC_JFE_HS_327T

description: Gene expression data from HCC


title: ICC_JFE_HS_373T

description: Gene expression data from HCC


title: ICC_JFE_HS_312T

description: Gene expression data from HCC


title: ICC_JFE_HS_397T

description: Gene expression data from HCC


title: ICC_JFE_HS_376T

description: Gene expression data from HCC


title: ICC_JFE_HS_345T

description: Gene expression data from HCC


title: ICC_JFE_HS_415T

description: Gene expression data from HCC


title: ICC_JFE_HS_409T

description: Gene expression data from HCC


title: ICC_JFE_HS_358T

description: Gene expression data from HCC


title: ICC_JFE_HS_418T

description: Gene expression data from HCC


title: ICC_JFE_HS_344T

description: Gene expression data from HCC


title: ICC_JFE_HS_338T

description: Gene expression data from HCC


title: ICC_JFE_HS_374T

description: Gene expression data from HCC


title: ICC_JFE_HS_414T

description: Gene expression data from HCC


title: ICC_JFE_HS_405T

description: Gene expression data from HCC


title: ICC_JFE_HS_402T

description: Gene expression data from HCC


title: ICC_JFE_HS_399T

description: Gene expression data from HCC


title: ICC_JFE_HS_352T

description: Gene expression data from HCC


title: ICC_JFE_HS_347T

description: Gene expression data from HCC


title: ICC_JFE_HS_350T

description: Gene expression data from HCC


title: ICC_JFE_HS_354T

description: Gene expression data from HCC


title: ICC_JFE_HS_332T

description: Gene expression data from HCC


title: ICC_JFE_HS_342T

description: Gene expression data from HCC


title: ICC_JFE_HS_337T

description: Gene expression data from HCC


title: ICC_JFE_HS_355T

description: Gene expression data from HCC


title: ICC_JFE_HS_351T

description: Gene expression data from HCC


title: ICC_JFE_HS_406T

description: Gene expression data from HCC


title: ICC_JFE_HS_346T

description: Gene expression data from HCC


title: ICC_JFE_HS_401T

description: Gene expression data from HCC


title: ICC_JFE_HS_417T

description: Gene expression data from HCC


title: ICC_JFE_HS_336T

description: Gene expression data from HCC


title: ICC_JFE_HS_412T

description: Gene expression data from HCC


title: ICC_JFE_HS_419T

description: Gene expression data from HCC


title: ICC_JFE_HS_403T

description: Gene expression data from HCC


title: Control8

city: Shanghai

first: cheng

last: lu

state: Shanghai

address: Pudong New Area

country: China

institute: Shanghai University of Traditional Chinese Medicine

description: Gene expression after drug intervention

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.   On completion of the fragmentation reaction, 22.5 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE Microarray (8*60K) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.    After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with  Genespring 13.0(Agilent). Probe that at least 1out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: Cardiac tissue_8W

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The dosages administered were chosen according to the “Human and Animal Body Surface Area Dose Equivalent Conversion Ratio Table.” (Wojcikowski and Gobe, 2014). The animals were sacrificed 24 h after the last administration.

extract_protocol: RNA was prepared by mirVanaTM RNA Isolation Kit(Applied Biosysterm p/n AM1561) following the manufacturer's recommendations.

treatment_protocol: After one week of feeding, all experimental animals were administered AACO solution at 0.386 µg/g (TCM group),  or an equivalent amount of double-distilled water (control group), once daily for 8 weeks.

value: whole heart

value: control


title: Control5

description: Gene expression after drug intervention


title: ICC_JFE_HS_421T

description: Gene expression data from HCC


title: Case2_11

description: Gene expression after drug intervention

value: AACO


title: Case2_4

description: Gene expression after drug intervention


title: Case2_7

description: Gene expression after drug intervention


title: ICC_JFE_HS_426T

description: Gene expression data from HCC


title: ICC_JFE_HS_425T

description: Gene expression data from HCC


title: ICC_JFE_HS_364T

description: Gene expression data from HCC


title: Control1

description: Gene expression after drug intervention


title: ICC_JFE_HS_365T

description: Gene expression data from HCC


title: ICC_JFE_HS_436T

description: Gene expression data from HCC


title: ICC_JFE_HS_422T

description: Gene expression data from HCC


title: ICC_JFE_HS_431T

description: Gene expression data from HCC


title: ICC_JFE_HS_366T

description: Gene expression data from HCC


title: ICC_JFE_HS_433T

description: Gene expression data from HCC


title: ICC_JFE_HS_429T

description: Gene expression data from HCC


title: ICC_JFE_HS_423T

description: Gene expression data from HCC


title: ICC_JFE_HS_088G

description: Gene expression data from HCC


title: ICC_JFE_HS_359T

description: Gene expression data from HCC


title: ICC_JFE_HS_435T

description: Gene expression data from HCC


title: ICC_JFE_HS_370T

description: Gene expression data from HCC


title: ICC_JFE_HS_361T

description: Gene expression data from HCC


title: ICC_JFE_HS_424T

description: Gene expression data from HCC


title: ICC_JFE_HS_368T

description: Gene expression data from HCC


title: ICC_JFE_HS_371T

description: Gene expression data from HCC


title: ICC_JFE_HS_437T

description: Gene expression data from HCC


title: PRAD_meta_brain

type: genomic

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

country: Germany

institute: Charité - Universitätsmedizin

hyb_protocol: Samples were hybridized to Infinium Human Methylation EPIC BeadChips (Illumina) v1 and v2 according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: We performed FunNorm (Minfi R package) and BMIQ (WateRmelon R package) normalization. We filtered probes non-cg probes, probes corresponding to SNPs, probes that align to multiple locations, and probes on sex chromosomes.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PRAD metastasis in brain, in house negative control

label_protocol: Supplier protocol (Illumina)

extract_protocol: Semi-automated DNA extraction was performed according to the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, Promega)

tag: tissue type

value: metastasis

tag: illumina methylation epic assay version


title: Organoid_PAAD_1

source_name: Organoid primary PAAD

value: organoid


title: STAD_meta_brain_2

source_name: STAD metastasis in brain, in house negative control


title: STAD_meta_brain_1


title: UCEC_meta_brain_2

source_name: UCEC metastasis in brain, in house negative control


title: LUAD_meta_brain_6

source_name: LUAD metastasis in brain, in house negative control


title: BRCA_meta_brain

source_name: BRCA metastasis in brain, in house negative control


title: LUAD_meta_brain_5


title: KJ080_6407

city: Richmond

first: Kaitlyn

middle: G

last: Jackson

state: Virginia

address: 7414 Seminary Ave

department: Immunology

institute: VCU

description: CDNW-SphK2 KO

hyb_protocol: hybridization of sample to NanoString probes for 16h at 65C in hybridization buffer, according to the manufacturer instructions

scan_protocol: scanning completed by NanoString nCounter Digital Analyzer

data_processing: Raw counts processed using nSolver Analysis Software; data normalization to internal reference probes and background subtraction performed using Rosalind Software

label: Nanostring metabolic panel barcode

source_name: Constitutive SphK2 KO

label_protocol: RNA target-specific barcoded probes

growth_protocol: Mice aged 12-18 weeks old were fed diet for 16 weeks prior to sacrifice

extract_protocol: Trizole method

treatment_protocol: diet feeding, ad libitum; see characteristics: Tag_ diet

tag: biological sex

value: male

tag: diet

value: control diet and normal water

value: SphK2 KO

tag: genetic background

tag: age (days)

tag: diet duration (weeks)


title: UCEC_meta_brain_1


title: Organoid_PAAD_meta_peritoneal_carcinomatosis

source_name: Organoid PAAD metastasis in the peritoneum


title: LUAD_meta_brain_7


title: KJ080_6552

description: CDNW-WT

source_name: Wild type control

tag: genotype

value: WT


title: KJ080_6551

description: WDSW-WT

value: Western diet and sugar water


title: PAAD_meta_peritoneal_carcinomatosis_11

hyb_protocol: Samples were hybridized to Infinium Human Methylation EPIC BeadChips (Illumina) according to the manufacturer’s protocol.

source_name: peritoneal carinomatosis, synchronous, imagistic suspect infiltrative mass in the pancreas head-body, diagnostic laparoscopy

value: PAAD

tag: location

value: peritoneum

tag: subject id

value: Pat 16


title: LUAD_meta_brain_2


title: KJ080_6123

description: WDSW-SphK2 KO


title: KJ080_6401

description: CDNW-SphK2 KO


title: LUAD_meta_brain_4


title: KJ080_6398

description: CDNW-SphK2 KO


title: KJ080_6503

description: WDSW-WT


title: KJ080_6122

description: WDSW-SphK2 KO


title: KJ080_6543

description: CDNW-WT


title: KJ080_6501

description: WDSW-WT


title: KJ080_6542

description: CDNW-WT


title: KJ080_6420

description: WDSW-SphK2 KO


title: LUAD_meta_brain_3


title: UNKNOWN_meta_brain

source_name: Unknown cancer metastasis in brain, in house negative control


title: Spleen, LPS, 24 h, rep3

city: Valdeolmos

first: Pedro

last: Perdiguero

state: Madrid

address: Ctra. de Algete a El Casar Km 8.1

department: Animal Health Research Centre

country: Spain

institute: CISA-INIA

data_processing:
Reads were trimmed and size filtered using Trimmomatic software v.0.39. A new filter step was applied to reads using SortMeRNA software. A quality check was performed using FastQC software.  Additional trimming step was applied deleting the first 10bp and the last 5bp for each read using the FastQ trimmer tool from the FastX toolkit.
Trinity software was used in different steps for de novo transcriptome assembly.
Reads from each sample were mapped independently against the final A. regius reference transcriptome using bowtie2 software
RNA-seq transcript abundances were estimated using RSEM software
DeSeq2 software was used for differential expression analysis.
Assembly: Reference transcriptome de novo assembled during study
Supplementary files format and content: Raw_Data_Matrix.txt is a text file containing raw data count for each sample
Supplementary files format and content: Argyrosomus_regius_reference_transcriptome.fasta is a multifasta file containing the final version of reference transcriptome

organism: Argyrosomus regius

source_name: Spleen

growth_protocol: Meagre (Argyrosomus regius) juveniles were obtained from IPMA (Olhão, Portugal) and acclimated for 2 weeks to the experimental conditions at the Marine Zoology Station, Porto University (Portugal) in a thermo-regulated recirculating water system (22 ◦C ± 1 ◦C).

extract_protocol:
The spleen was removed from 12 fsh pooled into 3 groups of 4 fish for each sampling point (4 and 24 h), both from PBS treated fish (control samples) and LPS treated fsh (experimental samples) at 4 h and 24 h after treatment [n = 3 (pools, 4 fish/pool)/treatment/sampling point)]
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) including an unique index per sample.

treatment_protocol: 10 μg/g fsh of lipopolysaccharides (LPS) extracted from Photobacterium damselae subsp. piscicida Lg41/01 or phosphate buffer saline (PBS).

tag: tissue

value: Spleen

tag: treatment

value: LPS


title: Spleen, LPS, 4 h, rep2

tag: time

value: 4 h


title: Spleen, PBS, 24 h, rep3

value: PBS


title: Spleen, LPS, 4 h, rep1


title: Spleen, PBS, 24 h, rep2


title: PMOC_meta_brain

source_name: PMOC metastasis in brain, in house negative control


title: PAAD_meta_peritoneal_carcinomatosis_10

source_name: peritoneal carinomatosis, synchronous, imagistic suspect infiltrative mass in the pancreas head

tag: disease

value: Pat 15


title: Spleen, PBS, 4 h, rep3


title: Spleen, LPS, 24 h, rep2


title: PAAD_meta_peritoneal_carcinomatosis_7

source_name: peritoneal carinomatosis, metachronous, 2 years prior resected pancreas head with confirmed PAAD

value: Pat 12


title: PAAD_meta_peritoneal_carcinomatosis_8

source_name: peritoneal carinomatosis, metachronous, 1 years prior resected pancreas head with confirmed PAAD

value: Pat 13


title: Spleen, PBS, 24 h, rep1


title: Spleen, PBS, 4 h, rep2


title: PAAD_meta_peritoneal_carcinomatosis_6

source_name: peritoneal carinomatosis, synchronous,  imagistic suspect infiltrative mass in the pancreas with suspected liver metastases

value: metastasis

value: Pat 8


title: Spleen, PBS, 4 h, rep1


title: PAAD_meta_lymph_node_metastasis_3

source_name: lymp node metastssis, synchronous,  Histologic confirmed and simultaneously resected PAAD with lymph node metastases

value: lymph node

value: Pat 11


title: Hfx. volcanii cells, rosR deletion strain, immunoprecipitation, rep3

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

library_source: genomic

data_processing:
50 bp reads were assessed for quality using FastQC and adapter sequences trimmed using Trim Galore and Cutadapt. Resultant reads were mapped to the Hfx. mediterranei ATCC3500 (assembly ASM30676v2; NCBI accession GCF_000306765.2) or Hfx. volcanii DS2 genome (ASM2568v1; GCF_000025685.1) using Bowtie2.
Sorting of mapped sequences was conducted using samtools. Sites of significant RosR binding enrichment were called using the MOSAiCS peak-calling package [REF] with sorted bam files as input. MOSAiCS parameters included fragment length (fragLen) 200, cap 0, PET false, analysis type IO, background estimate rMOM, FDR 0.01.
Using the DiffBind R package, peaks were considered reproducible if 100 bp of the reads in the peak overlapped across three of four biological replicate experiments. Using the GenomicRanges and IRanges R packages, a given peak was associated with a given genomic feature (gene or promoter region) if the they overlapped by 100 bp. Peaks that fell entirely inside promoter regions were associated with the nearest gene within 500 bp.
Peak-to-gene associations were then annotated using the corresponding NCBI genome annotation within the GenomicFeatures R package.
Assembly: Hfx. mediterranei ATCC3500 (assembly ASM30676v2; NCBI accession GCF_000306765.2); Hfx. volcanii DS2 genome (ASM2568v1; GCF_000025685.1)
Supplementary files format and content: sorted bam files

organism: Haloferax volcanii DS2

source_name: archaeal cells

growth_protocol: Each Hfx. strain (parental ΔpyrE and RosR::HA tagged) was grown in quadruplicate (ChIP-seq) in 50 mL rich medium until mid- to late-exponential phase (OD600 ~0.5-1.0).

extract_protocol:
chromatin immunoprecipitation (ChIP) and DNA extraction was conducted as previously described (Martinez Pastor M. et al., 2017).
For ChIP-seq, Libraries were constructed using the KAPA Hyper Prep kit using Illumina TruSeq adapters. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent).
Samples for each species were multiplexed according to the adapter mixtures and pooled. Each pool was run on a single lane on an Illumina HiSeq 4000 instrument by the Duke Sequencing and Genomics Techonology core facility

treatment_protocol: Crosslinking was performed by adding 37% formaldehyde (CH2O) for 20 min at room temperature.

value: archaeal cells

tag: cell line

tag: cell type

value: {delta}pyrE HVOrosR::HA

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: PAAD_meta_peritoneal_carcinomatosis_5

source_name: peritoneal carinomatosis, synchronous, imagistic suspect infiltrative mass in the pancreas with suspected liver and suprarenal metastases

value: PAAD

value: Pat 7


title: PAAD_meta_peritoneal_carcinomatosis_4

source_name: peritoneal carinomatosis, synchronous, clinical suspicion of pancreas carcinoma

value: peritoneum

value: Pat 6


title: PAAD_meta_lung_metastasis_2

source_name: lung metastasis, synchronous, imagistic suspect infiltrative mass in the pancreas

value: lung

value: Pat 10


title: PAAD_meta_peritoneal_carcinomatosis_9

source_name: peritoneal carinomatosis, synchronous, pancreas head resection with simultaneous metastasis in liver hilum

value: Pat 14


title: Hfx. volcanii cells, rosR deletion strain, whole cell extract control, rep4


title: Hfx. volcanii cells, rosR deletion strain, immunoprecipitation, rep1


title: Spleen, LPS, 24 h, rep1

value: Spleen

value: LPS


title: Hfx. volcanii cells, rosR deletion strain, immunoprecipitation, rep2


title: PAAD_meta_peritoneal_carcinomatosis_3

value: Pat 5


title: Hfx. volcanii cells, rosR deletion strain, whole cell extract control, rep2.


title: Hfx. volcanii cells, pyrE control, immunoprecipitation.

value: {delta}pyrE

value: standard growth medium, control strain


title: Hfx. volcanii cells, rosR deletion strain, whole cell extract control, rep3


title: PAAD_meta_lymph_node_metastasis_2

source_name: lymph node metastasis, synchronous, histologic confirmed and simultaneously resected PAAD with lymph node metastases

value: metastasis

value: lymph node

value: Pat 9


title: Hfx. volcanii cells, pyrE control, whole cell extract control.

value: archaeal cells


title: V2, scRNAseq

city: Guangzhou

first: Huang

last: Youhua

address: Wushan Street five road No. 483

institute: South China Agricultural University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (version 3.1.0).
Assembly: mm10
Supplementary files format and content: Matrix table raw gene counts for every gene and every cell

organism: Epinephelus lanceolatus

source_name: spleen

extract_protocol:
when more than 50% of the fish in the virus injected group showed clinical signs of disease three control and three diseased fish were sacrificed, and spleen were collected for single cell RNA-Seq analysis.
RNA libraries were prepared with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 according to the manufacter’s instructions.

value: spleen

value: Singapore grouper iridovirus (SGIV) injection


title: V1, scRNAseq

description: 10x Genomics


title: V3, scRNAseq

description: 10x Genomics


title: C4, scRNAseq

description: 10x Genomics

value: PBS injection


title: Hfx. volcanii cells, rosR deletion strain, whole cell extract control, rep1.

value: {delta}pyrE HVOrosR::HA

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: LUAD_meta_brain_1

source_name: LUAD metastasis in brain, in house negative control


title: Q_4_1

city: lanzhou

first: hongyan

last: Wang

state: gansu

address: No. 1 yingmen village, Anning district

department: College of Agronomy

institute: Gansu Agricultural University

description: Parallel sample 1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Codonopsis pilosula
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Codonopsis pilosula

source_name: leaf

growth_protocol: In this experiment, we used pots of soil-cultivated Codonopsis seedlings. The soil (moisture content was 150.43 g/kg) for the test was taken from the Bacchus Garden of Gansu Agricultural University. The test cultivars of C. pilosula were Weidang No. 1 (W1), a variety promoted in Dingxi, Gansu Province (the seed was obtained from the Dry Farming Research and Promotion Center of Dingxi, Gansu Province), and Gandang No. 1 (G1), a cultivar selected by the group of Yuan Chen and Feng-xia Guo of Gansu Agricultural University. All were naturally shade-dried seeds harvested in the same year. Each cultivar was potted in 10 pots, and a total of 20 pots were placed in the open-air experimental base of Gansu Agricultural University (with a rain-proof shed to prevent rainwater from entering) to ensure consistency with the local climatic conditions. The soil moisture content was maintained by weighing during the experimental stage (Ruiz-Nieto et al., 2015). All pots were periodically moved and rotated to minimize the effects of environmental heterogeneity (Ruiz-Nieto et al., 2015).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The weighing method was used to control the soil moisture content of potted plants at 180 ± 5 g/kg, and four weeks after the emergence of seeds, 2 pots of each cultivar were left as control (C, drought day 0). The remaining 8 pots of each cultivar were stopped from watering to conduct drought treatment (D); the day stopped from watering was drought day 0, and the weighing method was used to measure the soil moisture content. Three samples (2-pot mixes of each cultivar) were collected on drought days 0, 2, 4, 6, and 7 and stored at -80°C for subsequent physiological indicators, transcriptomics, and qRT-PCR assays.

value: leaf

value: Q4，pots of soil-cultivated Codonopsis seedlings


title: Q_4_2

description: Parallel sample 2


title: Q_4_3

description: Parallel sample 3


title: Q_2_3

description: Parallel sample 3

value: Q2，pots of soil-cultivated Codonopsis seedlings


title: C3, scRNAseq

description: 10x Genomics


title: Q_2_2

description: Parallel sample 2


title: G_4_3

description: Parallel sample 3

value: Q4，pots of soil-cultivated Codonopsis seedlings，drought


title: G_2_2

description: Parallel sample 2

value: Q2，pots of soil-cultivated Codonopsis seedlings，drought


title: PAAD_meta_lung_metastasis_1

source_name: lung metastasis, syncronous, Imagistic suspect mass in the pancreas

value: PAAD

value: lung

value: Pat 2


title: G_4_1

description: Parallel sample 1


title: G_2_3

description: Parallel sample 3


title: G_4_2

description: Parallel sample 2


title: Q_2_1

description: Parallel sample 1


title: C1, scRNAseq

description: 10x Genomics


title: G_2_1

description: Parallel sample 1


title: HEK293 cells, Flag-ZNF184 overexpression

city: Suwon

first: Jooho

last: shin

state: Gyeonggi-do, Republic of Korea

address: 2066 Seoburo

country: South Korea

institute: Sungkyunkwan University, School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Flag-tagged ZNF184 was transfected into HEK293 cells using XtremeGene transfection reagent (Roche Holding AG, Basel, Switzerland) in Opti-MEM medium.

value: ZNF184 overexpression


title: HEK293 cells, Control

value: human kidney (embryonic), Epithelial

value: WT


title: Day5_WT

first: Jana

last: Cable

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

description: 10X Genomics

data_processing:
Reads were aligned to hg38 with concatentated EBV Type 1 genome (NC007605)
Sam files were converted to bam files
bam files were used to generate count matrix with Rsubread
Normalized z scores were calculated with DESeq2
Assembly: hg38 with concatentated EBV Type 1 genome (NC007605)
Supplementary files format and content: csv file contains raw counts for each sample

source_name: B cells

extract_protocol:
RNA was extracted using Rneasy mini (Qiagen)
Librarys were constructed with NEBNext Ultra II RNA Library Prep Kit

value: B cells

value: WT Infected

tag: days post_infection


title: Day8_WT

description: 10X Genomics


title: Day0_Uninfected

description: 10X Genomics

value: Uninfected


title: Day5_LPKO

description: 10X Genomics

value: LPKO Infected


title: Day 2_WT

description: 10X Genomics


title: Day8_LPKO

description: 10X Genomics


title: SAMN32641505_Ctrl, scRNA-seq

city: Tallahassee

first: Li

last: Guo

address: Thrasher Medical Researcher Building, Suite 2300-D

department: College of Medicine

institute: Florida State University

description: 10X Genomics

data_processing:
FASTQ files were aligned to the GRCH38 using Cell Ranger v7.1.0. The raw gene expression matrices were input to Soup X 1.6.2 for ambient RNA removal using autoEstCont and adjustCounts to estimate and remove the contamination fraction.
Data quality control, filtering, dimensionality reduction, clustering, and differential expression analysis were conducted using Seurat v5.0.1 with ambient RNA removed data. Briefly, cells were filtered based on nFeature_RNA > 200, percent.mt < 10, and nCount_RNA < 10,000. Data normalization and batch effect correction were performed using IntegrateLayers function with CCAIntegration method. Dimensionality reduction and cell clustering were carried out sequentially with RunPCA, RunUMAP, FindNeighbors, and FindClusters. Cell types were classified based on the expression of canonical pancreatic markers within each cluster, supplemented by Azimuth reference mapping to refine the cell type identification.
Assembly: GRCH38
Supplementary files format and content: seurat objects containing gene expression matrix post ambient RNA removal, cell clustering, and other metadata

source_name: pancreas

extract_protocol:
Cultured islets were dissociated with TrypLE at 37oC for 9 minutes with manual trituration every 2 minutes.
scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 3′ Reagent Kits v 3.1 (PN-1000128, 10x Genomics) according to the user guide (CG000204, 10x Genomics).
scRNA-seq, Sequencing was carried out as paired-end (PE28x88) using a combination of Illumina NovaSeq 6000 and NovaSeq X Plus.

treatment_protocol: Human islets were cultured for 48 hours under either 5.1mM glucose (control) or 25mM glucose + 0.5mM palmitic acid (glucolipotoxicity condition).

value: pancreas

value: islet cells

value: control


title: SAMN32641505_GL, scRNA-seq

description: 10X Genomics

value: GL


title: HP23098_Researcher.1_GL.rds, scRNA-seq

description: 10X Genomics


title: HP23098_Researcher.2_Ctrl, scRNA-seq

description: 10X Genomics


title: PAAD_meta_liver_metastasis_1

source_name: liver metastasis, metachronous, 2 years prior, resected pancreas tail with confirmed PAAD.

tag: tissue type

value: primary

tag: specimen

value: resection

value: liver

value: Pat 3


title: PAAD_meta_peritoneal_carcinomatosis_2

source_name: peritoneal carinomatosis, synchronous, simultaneous resection of pancreas tail with confirmed PAAD

value: PAAD

value: metastasis

value: peritoneum

value: Pat 4


title: HP23098_Researcher.1_Ctrl.rds, scRNA-seq

description: 10X Genomics


title: PAAD_meta_peritoneal_carcinomatosis_1

source_name: peritoneal carcinomatosis syncronous, Imagistic suspect infiltrative mass in the pancreas head

value: Pat 1


title: Spleen, LPS, 4 h, rep3

source_name: Spleen

value: Spleen

value: LPS

value: 4 h


title: HP22286_GL, scRNA-seq

description: 10X Genomics


title: CITH107_GL, scRNA-seq

description: 10X Genomics


title: HPV- LNMT1

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

institute: Pusan National University

description: Fresh frozen sequencing

data_processing:
The cell stocks were thawed at 37℃ in 10% fetal bovine serum (FBS) and Dulbecco’s Modified Eagle Medium (DMEM). The cells were then rinsed twice with cold 0.04% bovine serum albumin (BSA) solution in phosphate-buffered saline (PBS) without calcium and magnesium ions and centrifuged at 300 g for 5 minutes at 4°C. Next, the samples were gently mixed in the same cold BSA/PBS solution without calcium and magnesium ions; the cell count was determined using a LUNA-FX7 automated fluorescence cell counter (Logos Biosystems) with acridine orange (AO) and propidium iodide (PI) staining.
Assembly: human reference genome
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered feature barcode matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefators in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatical transcriptome

source_name: HNSCC primary tumor

extract_protocol:
Tissue samples were collected from the primary tumor (PT) and paired lymph node metastasis tumor (LNMT) for ST sequencing, following a protocol approved by the Ethics Committee of Ajou University Hospital.
The final visible spatial gene expression data consisted of various components, including the standard Illumina P5 i5 index, spatial barcode, 12 bp UMI (Unique Molecular Identifier), cDNA fragment, i7 index, and standard Illumina P7.

value: HNSCC primary tumor


title: CITH107_Ctrl, scRNA-seq

description: 10X Genomics

value: pancreas


title: HPV- PT1

description: Fresh frozen sequencing


title: HP23098_Researcher.2_GL, scRNA-seq

description: 10X Genomics

value: islet cells


title: HPV+ PT3

description: Fresh frozen sequencing


title: N2-S-MB-BCR

city: Hang Zhou

first: Zeli

last: Zhang

address: ZhuanTang Jie Dao Shi long Shan Lu Nr. 17

institute: Westlake University

description: 10X Gemomics

data_processing:
The raw fastq files were processed using the 10X Genomics CellRanger (7.1.0) pipeline. The cell quality control, clustering, and marker gene analysis were performed by using Seurat (v4.3.0).
Assembly: hg18 and IMGT
Supplementary files format and content: Tab-separeted values files, matrix files, and VDJ assemble file

source_name: PBMC

extract_protocol:
B cells were isolated from previously frozen PBMCs by immunomagnetic negative selection according to the manufacturer’s protocol (EasySep Human B Cell Enrichment Kit, STEMCELL). The purified B cells were first stained with 1200 ng N1-M5 or N2-M5 probes (600 ng per color) for 30 min at 4 ˚C, then stained with CD20, CD19, CD27, IgD, and L/D blue. The live NA-specific MBCs were sorted into the FCS buffer and directly loaded on a 10X Chromium A chip.
Single-cell lysis and cDNA synthesis were performed by using the 5’ library and gel bead kit according to the provided protocol. The first-strand cDNA of 10X Barcoded was purified by silane magnetic beads, and sufficient mass was obtained by PCR amplification. The PCR products were quantified and qualified by Qubit3.0 Fluorometer (Invitrogen) and Agilent 2100 Bioanalyzer (Agilent). Then, the transcriptome and VDJ library preparation is performed by using 10X Chromium Single Cell VDJ Kits. All libraries were quantified by using Qsep100 (Bioptic) and Qubit3.0 Fluorometer (Invitrogen). Then libraries with different indices were multiplexed and loaded on an Illumina NovaSeq

value: PBMC

value: B cell


title: N1-S-MB

description: 10X Gemomics


title: HPV- LMNT2

description: Fresh frozen sequencing


title: HPV- PT2

description: Fresh frozen sequencing


title: HP22286_Ctrl, scRNA-seq

description: 10X Genomics

value: control


title: NI_TJ3_43_1 [Tumor] [Baseline]

city: Philadelphia

first: Adam

last: Luginbuhl

state: PA

address: 925 chestnut Street

department: Otolaryngology

institute: Thomas Jefferson University

description: Column BF

data_processing:
RNA-seq reads were aligned using Kallisto v0.42.4 to GENCODEv23 with default parameters. Gene expression was quantified for 20,062 protein-coding genes as transcripts per million (TPM) and log2-transformed values.
Assembly: GRCh38 (GENCODE v23)
Supplementary files format and content: Tab-delimited text file includes Log2 TPM values for each sample.

source_name: Squamous cell carcinoma

extract_protocol:
Nucleic acids were isolated by using Qiagen AllPrep DNA/RNA/microRNA Univerasl kits.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following manufacturer's protocols.

value: Squamous cell carcinoma

value: Subject 43 first of 2 timepoints

value: Pre-treatment


title: NI_TJ3_42_2 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column BE

value: Subject 42 second of 2 timepoints

value: Nivolumab and IDO-inhibitor


title: NI_TJ3_49_1 [Tumor] [Baseline]

description: Column BM

value: Subject 49 first of 2 timepoints


title: NI_TJ3_44_2 [Tumor] [Surgery] [Primary Path Response_Respoder] [Not a matched pair.]

description: Column BH

value: Subject 44 Post-treatment only. Primary Path Response_Respoder


title: NI_TJ3_42_1 [Tumor] [Baseline]

description: Column BD

value: Subject 42 first of 2 timepoints


title: NI_TJ3_47_1 [Tumor] [Baseline] [Not a matched pair.]

description: Column BK

value: Subject 47 Pre-treatent only. Future Primary Path Response_complete responder.


title: NI_TJ3_50_1 [Tumor] [Baseline]

description: Column BO

value: Subject 50 first of 2 timepoints


title: NI_TJ3_49_3 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column BN

value: Subject 49 second of 2 timepoints

value: Nivolumab


title: NI_TJ3_45_31A [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column BJ

value: Subject 45 second of 2 timepoints


title: NI_TJ3_50_12NO [Tumor] [Surgery]  [Primary Path Response_Non-Responder]

description: Column BP

value: Subject 50 second of 2 timepoints


title: NI_TJ3_43_3 [Tumor] [Surgery] [Primary Path Response_Complete Responder]

description: Column BG

value: Subject 43 second of 2 timepoints


title: NI_TJ3_48_1 [Tumor] [Baseline] [Not a matched pair.]

description: Column BL

value: Subject 48 Pre-treatment only. Future Primary Path Response_non-responder.


title: NI_TJ3_45_1 [Tumor] [Baseline]

description: Column BI

value: Subject 45 first of 2 timepoints


title: N1-S-MB-BCR

description: 10X Gemomics

value: PBMC

value: B cell


title: NI_TJ3_41_2 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column BC

value: Squamous cell carcinoma

value: Subject 41 second of 2 timepoints


title: NI_TJ3_41_1 [Tumor] [Baseline]

description: Column BB

value: Subject 41 first of 2 timepoints

value: Pre-treatment


title: HPV+ LNMT3

description: Fresh frozen sequencing

value: HNSCC primary tumor


title: Hfx. volcanii cells, rosR deletion strain, immunoprecipitation, rep4

source_name: archaeal cells

value: archaeal cells

value: {delta}pyrE HVOrosR::HA

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: NI_TJ3_40_3 [Tumor] [Surgery] [Primary Path Response_Respoder]

description: Column BA

value: Subject 40 second of 2 timepoints


title: NI_TJ3_40_1 [Tumor] [Baseline]

description: Column AZ

value: Subject 40 first of 2 timepoints


title: NI_TJ3_38_24J [Tumor] [Surgery] [Primary Path Response_Respoder]

description: Column AY

value: Subject 38 second of 2 timepoints

value: Nivolumab and IDO-inhibitor


title: NI_TJ3_37_3 [Tumor] [Surgery] [Primary Path Response_Complete Respoder]

description: Column AW

value: Subject 37 second of 2 timepoints


title: NI_TJ3_37_1 [Tumor] [Baseline]

description: Column AV

value: Subject 37 first of 2 timepoints


title: NI_TJ3_38_1 [Tumor] [Baseline]

description: Column AX

value: Subject 38 first of 2 timepoints


title: NI_TJ3_51_1 [Tumor] [Baseline] [Not a matched pair.]

description: Column BQ

value: Subject 51 Pre-treatment only. Future Primary Path Response_non-responder.


title: NI_TJ3_36_3 [Tumor] [Surgery] [Primary Path Response_minor Responder]

description: Column AU

value: Subject 36 second of 2 timepoints


title: NI_TJ3_36_1 [Tumor] [Baseline]

description: Column AT

value: Squamous cell carcinoma

value: Subject 36 first of 2 timepoints


title: NI_TJ3_35_1 [Tumor] [Baseline]

description: Column AR

value: Subject 35 first of 2 timepoints


title: NI_TJ3_33_3 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column AQ

value: Subject 33 second of 2 timepoints

value: Nivolumab


title: NI_TJ3_31_1 [Tumor] [Baseline] [Not a matched pair.]

description: Column AO

value: Subject 31 Pre-treatment only. Future Primary Path Response_Non-responder.

value: Pre-treatment


title: NI_TJ3_33_1 [Tumor] [Baseline]

description: Column AP

value: Subject 33 first of 2 timepoints


title: NI_TJ3_28_2 [Tumor] [Surgery] [Primary Path Response_Non-Respoder]

description: Column AL

value: Subject 28 second of 2 timepoints


title: NI_TJ3_23_1 [Tumor] [Baseline]

description: Column AE

value: Subject 23 first of 2 timepoints


title: NI_TJ3_20_2 [Tumor] [Surgery] [Primary Path Response_Non-Responder]

description: Column AB

value: Subject 20 second of 2 timepoints


title: NI_TJ3_23_3 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column AF

value: Subject 23 second of 2 timepoints

value: Nivolumab and IDO-inhibitor


title: NI_TJ3_29_1 [Tumor] [Baseline]

description: Column AM

value: Subject 29 first of 2 timepoints


title: NI_TJ3_27_1 [Tumor] [Baseline]

description: Column AI

value: Subject 27 first of 2 timepoints


title: NI_TJ3_20_1 [Tumor] [Baseline]

description: Column AA

value: Subject 20 first of 2 timepoints


title: NI_TJ3_24_1 [Tumor] [Baseline]

description: Column AG

value: Subject 24 first of 2 timepoints


title: NI_TJ3_22_2 [Tumor] [Surgery] [Primary Path Response_Respoder]

description: Column AD

value: Squamous cell carcinoma

value: Subject 22 second of 2 timepoints


title: NI_TJ3_29_3 [Tumor] [Surgery] [Primary Path Response_Complete Respoder]

description: Column AN

value: Subject 29 second of 2 timepoints


title: NI_TJ3_24_2 [Tumor] [Surgery] [Primary Path Response_Non-Responder]

description: Column AH

value: Subject 24 second of 2 timepoints


title: NI_TJ3_17_2 [Tumor] [Surgery] [Primary Path Response_Complete Respoder]

description: Column X

value: Subject 17 second of 2 timepoints

value: Nivolumab


title: NI_TJ3_19_1 [Tumor] [Baseline]

description: Column Y

value: Subject 19 first of 2 timepoints

value: Pre-treatment


title: NI_TJ3_17_1 [Tumor] [Baseline]

description: Column W

value: Subject 17 first of 2 timepoints


title: NI_TJ3_19_3 [Tumor] [Surgery] [Primary Path Response_Respoder]

description: Column Z

value: Subject 19 second of 2 timepoints


title: NI_TJ3_16_4 [Tumor] [Surgery] [Primary Path Response_Complete Respoder]

description: Column V

value: Subject 16 second of 2 timepoints


title: NI_TJ3_16_1 [Tumor] [Baseline]

description: Column U

value: Subject 16 first of 2 timepoints


title: NI_TJ3_15_2 [Tumor] [Surgery] [Primary Path Response_Respoder]

description: Colmun T

value: Subject 15 second of 2 timepoints

value: Nivolumab and IDO-inhibitor


title: NI_TJ3_15_1 [Tumor] [Baseline]

description: Column S

value: Subject 15 first of 2 timepoints


title: NI_TJ3_35_2 [Tumor] [Surgery] [Primary Path Response_Non-Responder]

description: Column AS

value: Subject 35 second of 2 timepoints


title: NI_TJ3_13_1 [Tumor] [Baseline]

description: Column Q

value: Subject 13 first of 2 timepoints


title: NI_TJ3_22_1 [Tumor] [Baseline]

description: Column AC

value: Squamous cell carcinoma

value: Subject 22 first of 2 timepoints


title: NI_TJ3_27_2 [Tumor] [Surgery] [Primary Path Response_Non-Respoder]

description: Column AJ

value: Subject 27 second of 2 timepoints


title: NI_TJ3_12_2 [Tumor] [Surgery] [Primary Path Response_Non-Responder]

description: Column P

value: Subject 12 second of 2 timepoints


title: NI_TJ3_28_1 [Tumor] [Baseline]

description: Column AK

value: Subject 28 first of 2 timepoints


title: NI_TJ3_11_1 [Tumor] [Baseline] [Not a matched pair.]

description: Column N

value: Subject 11 Pre-treatment only. Future Primary Path Response_Non-responder.


title: NI_TJ3_04_2 [Tumor] [Surgery] [Primary Path Response_Complete Responder]

description: Column H

value: Subject 4 second of 2 timepoints

value: Nivolumab


title: NI_TJ3_02_2 [Tumor] [Surgery] [Primary Path Response_minor Responder]

description: Column F

value: Subject 2 second of 2 timepoints


title: NI_TJ3_08_1 [Tumor] [Baseline]

description: Column K

value: Subject 8 first of 2 timepoints

value: Pre-treatment


title: NI_TJ3_02_1 [Tumor] [Baseline]

description: Column E

value: Subject 2 first of 2 timepoints


title: NI_TJ3_06_1 [Tumor] [Baseline]

description: Column I

value: Subject 6 first of 2 timepoints


title: NI_TJ3_08_2 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column L

value: Subject 8 second of 2 timepoints

value: Nivolumab and IDO-inhibitor


title: NI_TJ3_09_1 [Tumor] [Baseline] [Not a matched pair.]

description: Column M

value: Subject 9 Pre-treatment only. Future Primary Path Response_Responder.


title: NI_TJ3_13_2 [Tumor] [Surgery] [Primary Path Response_Respoder]

description: Column R

value: Subject 13 second of 2 timepoints


title: NI_TJ3_04_1 [Tumor] [Baseline]

description: Column G

value: Squamous cell carcinoma

value: Subject 4 first of 2 timepoints


title: NI_TJ3_01_3 [Tumor] [Surgery] [Primary Path Response_minor Respoder]

description: Column D

value: Subject 1 second of 2 timepoints


title: Day2_LPKO

description: 10X Genomics

value: B cells

value: LPKO Infected


title: WJL4662_RLF_N039

city: Stanford

first: Jinglong

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg19
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS, JoinT-seq

growth_protocol: K562 and its derived cell lines were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4). HEK293T and its derived cell lines were cultured at 37 °C and 5% CO2 in DMEM supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1/G0-arrested K562 and K562 ERCC6L2-/- cell lines were treated by 50 μM Palbociclib. The K562 G1/G0-arrested cells were nucleofected with pX330-Cas9-sgRNA to generated twined DSBs. The HEK293T-iCas9 cells were transfected with pMCB320-sgRNA to generated genome-wide DSBs.

value: lymphoblast cells

value: Palbociclib 50μM

tag: dsb induction_(bait_site)

tag: dsb induction_(prey_sites)


title: WJL4661_RLF_N039


title: WJL4670_RLF_N039

value: epithelial-like cells


title: WJL4667_RLF_N039


title: WJL4665_RLF_N039

value: WT


title: WJL4666_RLF_N039


title: WJL4664_RLF_N039


title: WJL4657_RLF_N039


title: WJL4659_RLF_N039


title: WJL4658_RLF_N039


title: WJL4660_RLF_N039


title: WJL4671_RLF_N039


title: WJL4668_RLF_N039


title: NI_TJ3_12_1 [Tumor] [Baseline]

description: Column O

value: Subject 12 first of 2 timepoints


title: NI_TJ3_06_3 [Tumor] [Surgery] [Primary Path Response_Non-Responder]

description: Column J

value: Subject 6 second of 2 timepoints


title: WJL4656_RLF_N039


title: NI_TJ3_01_1 [Tumor] [Baseline]

description: Column C

value: Subject 1 first of 2 timepoints

value: Pre-treatment


title: WJL4669_RLF_N039


title: WJL4654_RLF_N039


title: WJL4655_RLF_N039


title: Donor P013, section 2

city: Cape Town

first: Dorit

last: Hockman

address: Anzio Road

department: Department of Human Biology

country: South Africa

institute: University of Cape Town

description:
P13_3_V2_Visium
10x Genomics Visium on frozen tissue sections

data_processing:
Brightfield images of the stained sections were captured using an EVOS M5000 microscope (Thermo Fisher Scientific) at 20x magnification without coverslipping. Overlapping images of the sections including the fiducial frame were stitched together using Microsoft Image Composite Editor (V2.0.3)
10X Genomics Space Ranger count (10X Space Ranger V1.3.0) was used to perform alignment of FASTQ files to the human reference transcriptome (GRCh38), tissue detection, fiducial detection and barcode/UMI counting.
Cell2location (V.0.7a0) was used to spatially map the brain cell types by integrating the Visium data count matrices (Space Ranger output) with the associated annotated snRNAseq datasets (see accompanying paper) to generate Steyn_etal_sp.h5ad
Assembly: GRCh38
Supplementary files format and content: tiff image files of H&E stained tissue sections
Supplementary files format and content: Cell2Location model
Library strategy: Spatial Transcriptomics

source_name: temporal cortex

extract_protocol:
Tissue blocks containing the full span from pia to white matter were embedded in optimal cutting temperature compound (OCT) and stored at -80°C. The OCT-embedded samples were flash frozen in a 10×10 mm2 cryomold which was either frozen directly in liquid nitrogen or placed in a container of isopentane (Merck) which was in turn placed in liquid nitrogen at the same level as the isopentane.  10 μm-thick sections were cut from frozen blocks using a cryostat (Leica CM1860/CM1950) and collected onto the Spatial Gene Expression slide capture areas.  Hematoxylin and Eosin (H&E) staining was performed on Visium Spatial Gene Expression slides as detailed in the 10x Genomics demonstrated protocol guide CG000160 Rev B. Visium libraries were prepared from the stained tissue sections following the Visium Spatial Gene Expression Reagents Kit User Guide (CG000239, Rev D). At Step 1.1 the tissue was permeabilised for 12 minutes as determined using the Visium Spatial Gene Expression Tissue Optimisation User Guide (CG000238, Rev D). At Step 3.2, cDNA was amplified using 20 cycles.
Visium Spatial Gene Expression Reagents Kit

value: temporal cortex

tag: age (years)


title: Donor P015, section 2

description:
P15_3_V2_Visium
10x Genomics Visium on frozen tissue sections


title: Donor P028, technical replicate 1, library preparation batch E

data_processing:
Fastq files were aligned to the human reference transcriptome (GRCh38) and quantified using the count function from the 10X Genomics Cell Ranger (V.6.1.1).
The resulting count matrices were processed using a pipeline adapted from the Harvard Chan Bioinformatics Core (https://hbctraining.github.io/scRNA-seq_online/). The filtered gene barcode matrix for each sample was imported into R (V.4.2.0) using the Read10X function from the Seurat (V.2.0). See accompanying paper for details of barcode filtering.
Assembly: GRCh38
Supplementary files format and content: Seurat Object containing filtered barcodes and the following metadata slots: [1] "nCount_RNA"  [2] "nFeature_RNA"  [3] "seq_folder"  [4] "nUMI"  [5] "nGene"  [6] "barcode_ident"  [7] "predicted_doublet"  [8] "log10GenesPerUMI"  [9] "mitoRatio" [10] "sample" [11] "batch" [12] "sex" [13] "brain_region" [14] "biological_replicate" [15] "age_group" [16] "single_cell_chemistry" [17] "S.Score" [18] "G2M.Score" [19] "Phase" [20] "nCount_SCT" [21] "nFeature_SCT" [22] "seurat_clusters" [23] "high_resolution_MTG_annotation" [24] "high_resolution_MTG_annotation_cluster_colour" [25] "broad_cell_type"

extract_protocol:
Nuclei were isolated according to a protocol adapted from Habib et al. (2017) and the 10X Genomics nuclei isolation protocol (CG000124, User Guide Rev E)
10x Genomics Chromium Next Gem Single Cell 3’ Reagent Kit (v3.1)


title: Donor P029, technical replicate 1, library preparation batch G


title: Donor P013, section 1

description:
P13_3_V1_Visium
10x Genomics Visium on frozen tissue sections


title: Donor P015, section 1

description:
P15_3_V1_Visium
10x Genomics Visium on frozen tissue sections


title: Donor P026, technical replicate 1, library preparation batch G


title: Donor P021, technical replicate 1, library preparation batch E


title: Donor P018, technical replicate 2, library preparation batch D


title: Donor P018, technical replicate 1, library preparation batch D


title: Donor P015, technical replicate 2, library preparation batch C


title: Donor P013, technical replicate 6, library preparation batch C


title: Donor P013, technical replicate 5, library preparation batch C


title: Donor P011, technical replicate 2, library preparation batch D


title: Donor P013, technical replicate 4, library preparation batch B


title: Donor P011, technical replicate 1, library preparation batch D


title: Donor P015, technical replicate 1, library preparation batch C


title: CD19-CAR-T cells, nt-KO, scRNAseq

city: Changsha

first: Zineng

last: Huang

state: Hunan

address: No.139 of Renmin middle Road

department: Department of Hematology

institute: The Second Xiangya Hospital

description: 10× Genomics

data_processing:
Sequencing data alignment and gene expression matrix were performed by cellranger 5.0.1 (10X Genomics, San Francisco, CA) by aligning them to a pre-built human reference genome hg38 and human gene annotation version 32 (Ensembl 92).
Assembly: hg38 genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
CAR-T cells were co-cultured with MEC1 at an E: T = 2:1 for 48 hours, and GFP-positive CAR-T cells were obtained via FACS.
Single-cell RNA-Seq was performed following manufacturer’s protocols (https://www.10xgenomics.com). In brief, single cell suspension at 1000 cells/μl in PBS was loaded onto a Chromium controller for GEM (Gel Beads-In-Emulsion) generation and barcoding. Gene expression library was constructed with the chromium single cell 3' reagent kit v2 (10x Genomics).

value: PBMCs

value: Human T cell

value: Cas9-nt-sgRNA(non-targeting control sgRNA) RNP complex was electroporated into CD19-CAR-T cells, and then nt-KO CD19-CAR-T cells were co-cultured with MEC1 cells at an Effector (E) to target (T) ratio of 2:1 for 48 hours before Fluorescence-activated cell sorting


title: Donor P013, technical replicate 2, library preparation batch B


title: Donor P013, technical replicate 3, library preparation batch B


title: CD19-CAR-T cells, ITK-KO, replicate1

data_processing:
The adaptor sequence of RNA-seq raw reads was trimmed using trimmomatic-0.36, and reads were aligned to hg38 genome using HISAT2. Raw gene counts were generated using the subread featureCounts function.
Assembly: Hg38 genome
Supplementary files format and content: Space-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA extraction was performed for 1 × 10^6 sorted cells derived from each experimental group using the FastPure cell/tissue total RNA isolation kit (#RC112-01, Vazyme Biotech Co., Ltd.) according to the manufacturer’s instructions.
RNA libraries for RNA-Seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina

value: ITK deletion

value: Cas9-ITK-sgRNA(sgRNA designed to delete ITK) RNP complex was electroporated into CD19-CAR-T cells, and then ITK-KO CD19-CAR-T cells were co-cultured with MEC1 cells at an Effector (E) to target (T) ratio of 2:1 for 48 hours before Fluorescence-activated cell sorting


title: CD19-CAR-T cells, nt-KO, replicate3


title: Donor P013, technical replicate 1, library preparation batch B


title: CD19-CAR-T cells, nt-KO, replicate2


title: CD19-CAR-T cells, ITK-KO, replicate2


title: CD19-CAR-T cells, ITK-KO, replicate3

value: Cas9-ITK-sgRNA(sgRNA designed to delete ITK) RNP complex was electroporated into CD19-CAR-T cells, and then ITK-KO CD19-CAR-T cells were co-cultured with MEC1 cells  at an Effector (E) to target (T) ratio of 2:1 for 48 hours before Fluorescence-activated cell sorting


title: WJL4663_RLF_N039


title: CD19-CAR-T cells, nt-KO, replicate1


title: 178, S, biol rep 1

city: Vienna

first: Julia

last: Naas

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: 10x Genomics

data_processing:
Sequencing data of 10X libraries was processed using Cell Ranger software (V3.0.2, 10X Genomics). Cells were demultiplexed by cell line genotype using Souporcell (V2.4., DOI: 10.1038/s41592-020-0820-1) and two replicate organoids per cell line and protocol pooled for analysis. In experiments containing additional hash information, both hash information and genotypes were used for demultiplexing.
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: UMI count matrices (rows: genes, columns: cells)

source_name: brain organoid tissue

extract_protocol:
Organoids were dissociated at day 120 by incubation in a 9:1 mixture of Accutase (Sigma Aldrich, cat # A6954) and 10x Trypsin (Gibco, cat # 15400) at 37 °C on a Thermo-shaker (800 rpm) for approximately two hours and four units of TurboDNase (Thermo AM2238) were added after 30 min. After enzymatic dissociation, cells were filtered through a 35 µm strainer followed by dilution with 1% BSA in DPBS-/- (Biostatus; DR70250, 0.3 mM), counted and cells labeled (hashed) with TotalSeq™-A antibodies (biolegend) as required to allow demultiplexing of 4 samples either by genetic background or hash information per single cell transcriptomic reaction. For hashing, cells were stained for 30 min on ice, washed twice with 1% BSA in DPBS-/-.
After flow cytometry sorting a pool of equal cell numbers for each of the 4 samples was used as input for the Chromium Next GEM Single Cell 3’ Gene Expression (v3.1) following the 10x Genomics user guide.
10x Genomics Chromium Next GEM Single Cell 3' v3

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

tag: Sex

value: male

tag: protocol

value: striatum growth protocol (S)


title: 178, S, biol rep 2

description: 10x Genomics


title: 178, M, biol rep 2

description: 10x Genomics

value: midbrain growth protocol (M)


title: 178, D, biol rep 2

description: 10x Genomics

value: dorsal growth protocol (D)


title: 178, V, biol rep 2

description: 10x Genomics

value: ventral growth protocol (V)


title: 177, S, biol rep 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female


title: 178, D, biol rep 1

description: 10x Genomics


title: CD19-CAR-T cells, ITK-KO, scRNAseq

description: 10× Genomics

tag: genotype


title: 177, S, biol rep 1

description: 10x Genomics


title: 177, M, biol rep 1

description: 10x Genomics


title: 177, M, biol rep 2

description: 10x Genomics


title: 177, D, biol rep 1

description: 10x Genomics


title: 177, V, biol rep 2

description: 10x Genomics


title: 176, E2, M, biol rep 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)


title: 176, E2, D, biol rep 2

description: 10x Genomics


title: 176, E2, V, biol rep 1

description: 10x Genomics


title: 176, E2, V, biol rep 2

description: 10x Genomics


title: 176, E2, S, biol rep 1

description: 10x Genomics


title: 176, E1, S, biol rep 1

description: 10x Genomics


title: 176, E1, M, biol rep 1

description: 10x Genomics


title: 176, E2, M, biol rep 1

description: 10x Genomics


title: 176, E2, D, biol rep 1

description: 10x Genomics


title: 176, E1, M, biol rep 2

description: 10x Genomics


title: 176, E1, V, biol rep 1

description: 10x Genomics


title: 178, M, biol rep 1

description: 10x Genomics


title: 176, E1, V, biol rep 2

description: 10x Genomics


title: 176, E1, S, biol rep 2

description: 10x Genomics


title: 176, E1, D, biol rep 2

description: 10x Genomics


title: 176, E1, D, biol rep 1

description: 10x Genomics


title: UOFV_1, S, biol rep 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Uofv_1


title: UOFV_1, M, biol rep 2

description: 10x Genomics


title: UOFV_1, S, biol rep 1

description: 10x Genomics


title: UOFV_1, M, biol rep 1

description: 10x Genomics


title: UOFV_1, V, biol rep 2

description: 10x Genomics


title: 178, V, biol rep 1

description: 10x Genomics


title: UOFV_1, V, biol rep 1

description: 10x Genomics


title: 176, E2, S, biol rep 2

description: 10x Genomics


title: UOFV_1, D, biol rep 2

description: 10x Genomics


title: 177, V, biol rep 1

description: 10x Genomics


title: UOFV_1, D, biol rep 1

description: 10x Genomics


title: XUJA_2, S, biol rep 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2


title: XUJA_2, M, biol rep 2

description: 10x Genomics


title: XUJA_2, S, biol rep 1

description: 10x Genomics


title: XUJA_2, M, biol rep 1

description: 10x Genomics


title: XUJA_2, V, biol rep 1

description: 10x Genomics


title: XUJA_2, V, biol rep 2

description: 10x Genomics


title: XUJA_2, D, biol rep 2

description: 10x Genomics


title: ROZH_5, S, biol rep 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5


title: ROZH_5, D, biol rep 2

description: 10x Genomics


title: ROZH_5, S, biol rep 2

description: 10x Genomics


title: ROZH_5, V, biol rep 1

description: 10x Genomics


title: ROZH_5, M, biol rep 2

description: 10x Genomics


title: ROZH_5, M, biol rep 1

description: 10x Genomics


title: ROZH_5, D, biol rep 1

description: 10x Genomics


title: ROZH_5, V, biol rep 2

description: 10x Genomics


title: H9, S, biol rep 2

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)


title: H1, S, biol rep 2

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA01 (H1)


title: H9, M, biol rep 1

description: 10x Genomics


title: H9, D, biol rep 2

description: 10x Genomics


title: H9, D, biol rep 1

description: 10x Genomics


title: H9, M, biol rep 2

description: 10x Genomics


title: H1, S, biol rep 1

description: 10x Genomics


title: H1, M, biol rep 1

description: 10x Genomics


title: H1, M, biol rep 2

description: 10x Genomics


title: H1, V, biol rep 1

description: 10x Genomics


title: H1, D, biol rep 1

description: 10x Genomics


title: XUJA_2, V, day 120, biol repl 3, run 2

description: 10x Genomics

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

value: day 120

value: ventral protocol (V)


title: H1, D, biol rep 2

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1 )


title: XUJA_2, V, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: XUJA_2, V, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: H1, V, biol rep 2

description: 10x Genomics

value: male


title: XUJA_2, D, biol rep 1

description: 10x Genomics

value: dorsal growth protocol (D)


title: XUJA_2, S, day 80, biol repl 3, run 2

description: 10x Genomics

value: striatum protocol (S)


title: XUJA_2, S, day 120, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, V, day 13, biol repl 3, run 2

description: 10x Genomics

value: day 13


title: H9, S, biol rep 1

description: 10x Genomics

value: female

value: striatum growth protocol (S)


title: XUJA_2, S, day 40, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, S, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16


title: XUJA_2, M, day 120, biol repl 3, run 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: midbrain protocol (M)


title: XUJA_2, M, day 80, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, D, day 120, biol repl 3, run 2

description: 10x Genomics

value: dorsal protocol (D)


title: XUJA_2, M, day 16, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, M, day 40, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, pluripotent, day 0, biol repl 3, run 2

description: 10x Genomics

value: day 0


title: XUJA_2, D, day 25, biol repl 3, run 2

description: 10x Genomics

value: day 25


title: XUJA_2, D, day 40, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, V, day 25, biol repl 3, run 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: ventral protocol (V)


title: ROZH_5, V, day 40, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue


title: ROZH_5, V, day 80, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, V, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120


title: ROZH_5, V, day 13, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, V, day 25, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, S, day 120, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, S, day 16, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, S, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: ROZH_5, S, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: ROZH_5, pluripotent, day 0, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, M, day 80, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, M, day 120, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, M, day 40, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, M, day 16, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, D, day 120, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, D, day 40, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, D, day 80, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, D, day 25, biol repl 3, run 2

description: 10x Genomics


title: ROZH_5, D, day 13, biol repl 3, run 2

description: 10x Genomics


title: XUJA_2, D, day 13, biol repl 3, run 2

description: 10x Genomics


title: H9, V, day 120, biol repl 3, run 2

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)


title: CD8+ T-cells, CD44hi CD62L lo, TCR

city: Lebanon

first: Mary Jo

last: Turk

state: NH

address: 1 Medical Center Dr, Rubin FL7, Bench 33

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

data_processing:
FASTQ files were processed using Cellranger v7.1.0
Cellranger v7.1.0 was used generate the TCR file filtered_contig_annotations.csv
Assembly: mm10
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger TCR output files: filtered_contig_annotations.csv
Library strategy: scTCR-seq

source_name: Lymph node

extract_protocol:
Lymph nodes were mechanically dissociated and FACS sorted on CD44hi CD62Llo CD8+ endogenous cells and CD8+CD44hi Thy1.1+ Pmel cells.
Libraries were prepared using Illumina and 10x Genomics protocols

treatment_protocol: 5 mice per group, Untreated, Anti-CD4 treated, and immune checkpoint blockade treated (Anti-CTLA4 and Anti-PD1)

value: Lymph node

value: CD8+ CD44hi CD62L lo

value: Untreated, Anti-CD4 treated, or Anti-PD1+Anti-CTLA4 treated


title: CD8+ T-cells, CD44hi CD62L lo, HTO

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
FASTQ files were processed using Cellranger v7.1.0
Cellranger v7.1.0 was used generate the TCR file filtered_contig_annotations.csv
Assembly: mm10
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger TCR output files: filtered_contig_annotations.csv
Library strategy: HTO

molecule: protein


title: H9, V, day 40, biol repl 3, run 2

description: 10x Genomics

value: female


title: H9, V, day 80, biol repl 3, run 2

description: 10x Genomics


title: CD8+ T-cells, CD44hi CD62L lo, GEX

data_processing:
FASTQ files were processed using Cellranger v7.1.0
Cellranger v7.1.0 was used generate the TCR file filtered_contig_annotations.csv
Assembly: mm10
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger TCR output files: filtered_contig_annotations.csv


title: T_363_S41, Poly I:C,  anti-PD-1 and anti-C5aR1

city: Pamplona

first: Daniel

last: Ajona

state: Navarra

address: Adva Pio XII 55

institute: Cima-University of Navarra

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM31 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma (Processed data.xlsx)
Assembly: mm38
Supplementary files format and content: Processed data.xlsx

source_name: Tumor

growth_protocol: RPMI-1640 with Glutamax (Gibco), 10% Fetalclone (Thermo Fisher Scientific), 100 U/mL penicillin and 100 µg/mL streptomycin (Invitrogen). Cells were routinely tested for Mycoplasma.

extract_protocol:
RNA was then extracted with the NucleoSpin RNA isolation kit (Macherey-Nagel), according to manufacturer's instructions.
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Mice were then treated with vehicle, 1 mg/kg PMX53 (s.c.; daily starting on day 6), 100 μg anti-PD-1 (i.p.; days 7, 10 and 14) and/or 50 μg poly I:C (i.t.; days 11 and 15).

value: Tumor

value: Lewis Lung Cancer

value: Lung adenocarcinoma

value: WT

value: Poly I:C,  anti-PD-1 and anti-C5aR1


title: H9, V, day 25, biol repl 3, run 2

description: 10x Genomics

value: day 25


title: H9, V, day 13, biol repl 3, run 2

description: 10x Genomics

value: day 13


title: H9, S, day 120, biol repl 3, run 2

description: 10x Genomics

value: striatum protocol (S)


title: T_355_S43, Poly I:C,  anti-PD-1 and anti-C5aR1


title: T_362_S42, Poly I:C,  anti-PD-1 and anti-C5aR1


title: T_354_S47, Poly I:C,  anti-PD-1 and anti-C5aR1


title: H9, S, day 80, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue


title: T_353_S45, Poly I:C,  anti-PD-1 and anti-C5aR1


title: H9, M, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120

value: midbrain protocol (M)


title: T_331_S44, Poly I:C,  anti-PD-1 and anti-C5aR1


title: H9, S, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: D_373_S40, Poly I:C and anti-PD-1

value: Poly I:C and anti-PD-1


title: D_370_S38, Poly I:C and anti-PD-1


title: H9, M, day 80, biol repl 3, run 2

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: day 80


title: D_368_S36, Poly I:C and anti-PD-1


title: D_367_S35, Poly I:C and anti-PD-1


title: H9, D, day 120, biol repl 3, run 2

description: 10x Genomics

value: dorsal protocol (D)


title: H9, M, day 16, biol repl 3, run 2

description: 10x Genomics

value: female

value: day 16


title: D_366_S34, Poly I:C and anti-PD-1

value: Tumor

value: Lewis Lung Cancer


title: H9, D, day 80, biol repl 3, run 2

description: 10x Genomics


title: D_359_S39, Poly I:C and anti-PD-1

value: Lung adenocarcinoma

value: WT


title: H9, D, day 40, biol repl 3, run 2

description: 10x Genomics


title: D_344_S33, Poly I:C and anti-PD-1


title: T_360_S46, Poly I:C,  anti-PD-1 and anti-C5aR1

value: Poly I:C,  anti-PD-1 and anti-C5aR1


title: H9, D, day 25, biol repl 3, run 2

description: 10x Genomics

value: day 25


title: D_357_S37, Poly I:C and anti-PD-1


title: H9, S, day 16, biol repl 3, run 2

description: 10x Genomics

value: striatum protocol (S)


title: H1, V, day 120, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: ventral protocol (V)


title: H1, V, day 80, biol repl 3, run 2

description: 10x Genomics


title: H9, pluripotent, day 0, biol repl 3, run 2

description: 10x Genomics

value: day 0


title: C_375_S31, Control vehicle

value: Vehicle


title: C_361_S32, Control vehicle


title: H1, V, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: C_364_S28, Control vehicle


title: T_352_S48, Poly I:C,  anti-PD-1 and anti-C5aR1


title: C_356_S27, Control vehicle


title: H1, V, day 25, biol repl 3, run 2

description: 10x Genomics


title: C_351_S29, Control vehicle


title: C_369_S30, Control vehicle


title: H1, S, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120


title: C_339_S25, Control vehicle


title: H1, S, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: H9, M, day 40, biol repl 3, run 2

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female

value: midbrain protocol (M)


title: H1, V, day 13, biol repl 3, run 2

description: 10x Genomics

value: day 13


title: H1, S, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16


title: H1, S, day 40, biol repl 3, run 2

description: 10x Genomics


title: H9, D, day 13, biol repl 3, run 2

description: 10x Genomics

value: dorsal protocol (D)