title: P52-Baseline

first: Zhihua

last: Liu

state: Beijing

address: State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China

description:
Library name: P52-Baseline
whole.h5ad
whole_obs.csv

data_processing:
The Cell Ranger toolkit (version 6.1.0) provided by 10x Genomics was applied to aggregate raw data, filter low-quality reads, align reads to human reference genome (10X modified GRCh38, version 2020-A), assign cell barcodes, and generate the unique molecular identifier (UMI) matrix. A python-based toolkit, scanpy (version 1.9.1), was used for analyzing the scRNA-seq data. Specifically, the raw UMI matrixes of a total of 81 samples were firstly concatenated and then processed to filter out genes detected in less than 50 cells and cells with fewer than 500 genes or more than 50% counts of mitochondrial genes. For each sample, scrublet (version 0.2.3) was applied independently to identify doublets and remove, with an estimated doublet rate of 5%. The normalized expression matrix was calculated based on the raw UMI counts after normalizing total counts per cell (library size) and then scaled by 1e4 and log1p transformed.
Assembly: Human GRCh38
Supplementary files format and content: Expression h5ad file and cell annotation csv file

source_name: Esophagus tissue

extract_protocol:
Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Biopsy samples from each tumor at each time point were then combined before tissue disassociation. Samples were then collected in the RPMI-1640 medium (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37℃ according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-mm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit v2 from 10x Genomics, following the manufacturer’s instructions. In brief, single cells were washed once with PBS containing 0.04% bovine serum albumin (BSA) and resuspended in PBS containing 0.04% BSA to a final concentration of 500~1,200 cells/ml as determined by Rigel S2 cell counter (Countstar). ~10,000 cells were captured in droplets to generate nanoliter-scale Gel bead in EMulsion (GEMs). GEMs were then reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad) programmed at 53℃ for 45 min, 85℃for 5 min, and held at 4℃. After reverse transcription and cell barcoding, emulsions were broken and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Fisher Scientific), followed by PCR amplification.

value: Esophagus tissue

tag: sample type

value: Baseline


status: Public on Aug 10 2026

type: SRA

city: Bloomington

first: Cristina

last: Landeta

state: Indiana

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University

description:
Library name: DE-12266-Fadoli-CH12
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 12 h post-infection  replica C
Fadoli-CH12_S52

library_source: transcriptomic

data_processing:
The Illumina integrate system was used to separate the bar-coded sequences and demultiplex paired end reads into FASTQ files.
The pre-trimmed RNA-seq data was validated with FastQC (v0.11.5) and MultiQC (v1.33). The data was re-trimmed using fastp (v0.21.0).
The paired-end reads were them mapped using HISAT2 to the combined fasta files consisting of the Yasminevirus GU-2018, Fadolivirus algeromassiliense and the Vermamoeba vermiformis CDC-19.
The subread algorithm featureCounts was used to generate gene-level quantification.
The data was then processed through the R (v4.5.1) package deseq2 to identify differentially expressed genes.
Assembly: combined fasta files consisting of the Yasminevirus GU-2018 (NCBI), Fadolivirus algeromassiliense (NCBI), and the Vermamoeba vermiformis CDC-19
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with coding regions of the genes.

molecule: polyA RNA

organism: Vermamoeba vermiformis

growth_protocol: A suspension of V. vermiformis was prepared by successive cycles of centrifugation (3,000 × g for 10 min) and resuspension in starvation medium.

extract_protocol:
RNA extraction was performed as per manufacturer’s instructions with DNase treatement (Ozyme, Quick-RNA MiniPrep kit). mRNA was then captured with poly(A) tail using oligo(dT) coated magnetic beads following standard kit recommendations (NEBNext Poly(A) mRNA Magnetic Isolation Module, New England Biolabs).
After poly(A)+ RNA enrichment, a cDNA library was prepared using SuperScript IV Reverse Transcriptase (ThermoFisher), then a second brin synthesis was done using DNA Klenow I polymerase (New England Biolabs). cDNA libraries were done using COVIDSeq tests and sequenced using paired-end strategy (2*150 bp) using Illumina Novaseq Sequencer (Illumina Inc.).

treatment_protocol: Triplicates 30 mL cultures of amoebae at 106 cells/mL, quantified using an inverted microscope (Kovaslide), were inoculated with Yasminevirus or Fadolivirus at a multiplicity of infection (MOI) of 10 (TCID50 to quantify viral stocks were performed before infection cycles) in a 75-cm2 culture flask. After 30 min of incubation at 30°C for viral entry, the supernatant was carefully aspirated to remove extracellular Yasminevirus or Fadolivirus particles and maintain amoeba’ monolayers. The cells were resuspended in 10 mL of fresh medium for a second incubation at 30°C for 16 h. This time point was considered hour zero (H0). At H2, H4, H6, H8, H10, H12, and H16 of each triplicate amoebae were collected and after centrifugation of 0.5 mL aliquot the sample was used for RNA extraction.

tag: cell line

tag: cell type

value: Whole cells

tag: genotype

value: WT

tag: treatment

value: Fadolivirus infected

tag: time

value: 12 h post-infection


title: Human keratinocyte bulk RNA-seq, untreated control, donor 2, rep 1

city: San Francisco

first: Charlotte

last: Hurabielle

state: CA

address: 513 Parnassus Avenue

institute: University of California, San Francisco

description:
Library name: KC_RNAseq_Untreated_donor2_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: untreated control, applied daily from day 7 to day 14. Donor 2, technical replicate 1.

data_processing:
Raw FASTQ files were trimmed with fastp (v1.0.1) and quality-checked with FastQC and MultiQC (v1.32).
Transcript abundance was quantified by pseudoalignment to GRCh38 using Kallisto (v0.46.2). Gene-level abundance was estimated from transcript abundance using tximport (v1.34.0).
Differential gene expression was identified using DESeq2 (v1.46.0), modeling batch (donor) and cytokine treatment effects. Volcano plots were generated using adjusted DESeq2 outputs with ashr (v2.2-63).
Pre-ranked gene set enrichment analysis (GSEA) was performed using t-statistics from DESeq2 outputs with fgsea (v1.32.4) on GO ontology gene sets from MSigDB and custom gene sets.
Module scores were calculated using the AddModuleScore() function from Seurat (v5.3.1).
Assembly: GRCh38
Supplementary files format and content: Gene-level count matrix (tab-delimited .txt): rows are genes (Ensembl ID + gene symbol), columns are samples; values are estimated counts from tximport.
Supplementary files format and content: DESeq2 differential expression results tables (.csv): log2 fold change, Wald statistic, p-value, and adjusted p-value for each pairwise comparison.

organism: Homo sapiens

source_name: primary human keratinocyte

growth_protocol: Primary human keratinocytes were isolated from neonatal foreskins and expanded in T175 flasks to ~70% confluence. 500,000 cells were seeded into 12-well Millicell hanging inserts (0.4 um PET membrane; Millipore) pre-coated with CellStart (Invitrogen) diluted 1:10 in DPBS, using Epilife supplemented with Human Keratinocyte Growth Supplement (Gibco) as initial medium. At 72 hours (day 3), medium was switched to CNT-Prime Epithelial 3D Airlift Medium (CELLnTEC) in both apical and basal compartments. After 24 hours submerged, cultures were air-lifted by aspirating apical medium and reducing basal medium to 1.5 mL. From day 4, cultures were fed daily with 1 mL differentiation medium.

extract_protocol:
Total RNA was extracted from air-lifted 3D keratinocyte cultures at day 14.
Poly-A selected RNA libraries were prepared and sequenced as paired-end reads.

treatment_protocol: Beginning on day 7, cultures received one of the following daily supplements: IL-17A (10 ng/mL; BioLegend 570504), IFNg (10 ng/mL; BioLegend 713906), both (IL-17A 10 ng/mL + IFNg 10 ng/mL), or control medium alone. On day 12, cultures were transferred to a dry incubator to complete terminal differentiation. Cultures were harvested on day 14.

value: primary human keratinocyte

value: untreated control

tag: batch


title: P51-Treat

city: Beijing

department: State Key Laboratory of Molecular Oncology

country: China

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

description: Library name: P03-080

library_source: transcriptomic single cell

tag: tissue

tag: tumor stage


title: P51-Baseline

description: Library name: P03-080-LN4


description:
Library name: DE-12265-Fadoli-CH10
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 10 h post-infection  replica C
Fadoli-CH10_S51

value: 10 h post-infection


title: P50-Baseline

description: Library name: P03-080-LN2


title: Human keratinocyte bulk RNA-seq, untreated control, donor 1, rep 1

description:
Library name: KC_RNAseq_Untreated_donor1_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: untreated control, applied daily from day 7 to day 14. Donor 1, technical replicate 1.


title: P49-Baseline

description: Library name: P03-079


description:
Library name: DE-12264-Fadoli-CH8
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 8 h post-infection  replica C
Fadoli-CH8_S50

value: 8 h post-infection


title: P48-Treat

description: Library name: P03-074


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 4, rep 1

description:
Library name: KC_RNAseq_IFNg_donor4_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 4, technical replicate 1.

value: IFNg (10 ng/mL)


title: JR5558 mouse retina-2, 4 weeks

city: Eveleigh

first: Ting

last: Zhang

state: NSW

address: C81 Biomedical Building, 1 Central Ave

country: Australia

institute: The University of Sydney

description: Library name: Sample 8

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: Excel .xls file includes both raw read counts and FPKM-normalized gene expression values for each sample

molecule: total RNA

organism: Mus musculus

source_name: retina

extract_protocol:
Total RNA from the retinas of 4-week and 8-week-old JR5558 mice and age-matched C57BL/6 mice (n = 3) was extracted using a GenElute™ Single Cell RNA Purification Kit (RNB30, Sigma-Aldrich).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: retina


title: CITE-seq Sample 3

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Sample 3

data_processing:
The reads were processed with Cell Ranger version 6.1.1., which quantified transcript counts per putative cell. Quantification was performed using the STAR aligner against the GRCh38 transcriptome.
Assembly: hg38
Supplementary files format and content: Barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz files were created for samples 1, 2 and 3.
Library strategy: CITE-seq

source_name: Ocular surface

growth_protocol: Human donor eyes were obtained from eye banks. The eyes were dissected into three tissues: conjunctiva, limbus and central cornea. Epithelial cells from each tissue were obtained by Dispase II. After dissociation by TrypLE, the cells were used for CITE-seq.

extract_protocol:
The cells were loaded onto a single lane (Chromium chip) for encapsulation in lipid droplets using the Single Cell 3' kit V3.1. cDNA synthesis was performed according to the 10X Genomics protocol.
Gene expression and protein library generation were performed accotding to the 10X Genomics protocol.

value: Ocular surface

value: Ocular surface cells


title: P48-Baseline

description: Library name: P03-062


description:
Library name: DE-12263-Fadoli-CH6
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 6 h post-infection  replica C
Fadoli-CH6_S49

value: 6 h post-infection


title: P47-Treat

description: Library name: P03-061


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 2, rep 1

description:
Library name: KC_RNAseq_IFNg_donor2_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 2, technical replicate 1.


title: CITE-seq Sample 2

description: Library name: Sample 2


title: P47-Baseline

description: Library name: P03-053


title: C57BL/6J mouse retina-1, 8 weeks

description: Library name: Sample 4


title: P46-Treat

description: Library name: P03-051


title: CITE-seq Sample 1

description: Library name: Sample 1


title: P46-Baseline

description: Library name: P03-046


description:
Library name: DE-12262-Fadoli-CH4
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 4 h post-infection  replica C
Fadoli-CH4_S48

value: 4 h post-infection


description:
Library name: DE-12261-Fadoli-CH2
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 2 h post-infection  replica C
Fadoli-CH2_S47

value: 2 h post-infection


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 1, rep 2

description:
Library name: KC_RNAseq_IFNg_donor1_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 1, technical replicate 2.


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 1, rep 1

description:
Library name: KC_RNAseq_IFNg_donor1_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 1, technical replicate 1.


title: P45-Treat

description: Library name: P03-041

value: Esophagus tissue


title: C57BL/6J mouse retina-1, 4 weeks

description: Library name: Sample 1


title: C57BL/6J mouse retina-2, 4 weeks

description: Library name: Sample 2


title: P45-Baseline

description: Library name: P01-085


description:
Library name: DE-12260-Fadoli-CH0
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 30 min post-infection  replica C
Fadoli-CH0_S46

value: 30 min post-infection


title: SJRHB011_Y_DYE0730_VT

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
Library name: SJRHB000911_C6
2502292

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

source_name: Tumor

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

value: Tumor

value: VT

value: RMS


title: P44-Baseline

description: Library name: P01-080


title: SJRHB030730_X1_DYE0729_2D

description:
Library name: SJRHB030730_C2 Rep 2
2502291

source_name: Cells

value: Cells


title: P44-Treat

description: Library name: P01-081


title: P43-Treat

description: Library name: P01-079


title: Human keratinocyte bulk RNA-seq, untreated control, donor 4, rep 1

description:
Library name: KC_RNAseq_Untreated_donor4_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: untreated control, applied daily from day 7 to day 14. Donor 4, technical replicate 1.

value: primary human keratinocyte


title: SJRHB030730_X1_DYE0728_T0

description:
Library name: SJRHB030730_X1
2502290


title: P43-Baseline

description: Library name: P01-078


description:
Library name: DE-12259-YasmineTnegC
Vermamoeba vermiformis mock infected control for Yasminevirus samples  replica C
YasmineTnegC_S45

value: Whole cells

value: WT

value: mock infected

value: mock infected control


description:
Library name: DE-12258-Yasmine-CH16
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 16 h post-infection  replica C
Yasmine-CH16_S44

value: Yasminevirus infected

value: 16 h post-infection


title: LACO1_RNAseq

city: Shanghai

first: Zhaozhao

last: Zhao

address: Songhu Road 2005

institute: FUDAN UNIVERSITY

description: Library name: Sample3

data_processing:
Raw scRNA-seq data were processed using Cell Ranger (v8.0.1) from 10x Genomics (with Count functionality) for read alignment to the prebuilt GRCh38 genome reference. The resulting gene-by-cell unique molecular identifier (UMI) count matrix was analyzed using R package Seurat.  Code used for the assignment of cells to reference expression profiles is available at https://github.com/broadinstitute/single_cell_classification. Aligned BAM files were used as input for transcript-level peak calling with the SCAPTURE pipeline. The high-confidence PASs were used to construct a PAS-based GTF annotation, which was subsequently quantified using UMI-tools (v1.1.6) protocol. The final PAS-by-cell count matrix represented the expression of transcripts with distinct PASs at single-cell resolution. To assess the impact of JTE-607 treatment on transcriptomic heterogeneity, we calculated the diversity score for each treatment condition based on the PAS-based transcript expression profiles. We performed PCA to project the expression profiles of all cells, enabling the extraction of key features while minimizing noise. The top 30 PCs were selected. We performed 1,000 down-sampling analyses by randomly sampling 1,000 cells without replacement, and defined diversity as the average distance of the sampled cells to the centroid. To mitigate the influence of outliers on diversity score calculation, we excluded the cells with all the first three PCs exceeding 3 standard deviations from the mean.
Assembly: GRCh38
Supplementary files format and content: mtx file with raw UMI counts for every gene and cell. Does not have row or column names, these are found in the additional txt files
Supplementary files format and content: txt file with gene names;  txt file with cell barcodes and sample names. The sample name is separated from the barcode by an underscore

source_name: Lung cancer organoid

extract_protocol:
Samples were processed using the Chromium Single Cell 3′ (v2 Chemistry), platform with the target of ∼10,000 cells (10x Genomics) following manufacturer's instructions. Briefly, cells were added onto a chip to form Gel Bead-in-Emulsion (GEMs) in the Chromium instrument followed by cell lysis, barcoding, fragmentation, adaptor ligation and addition of sample index to the libraries before sequencing.
cDNA from GEMs was recovered and amplified by PCR. Subsequently, cDNA fragment length was optimized by enzymatic digestion and fragment screening. Finally, library construction was completed by end repair and addition of traditional second-generation sequencing junctions, and a standard sequencing DNA library was obtained by PCR amplification. High-throughput sequencing was performed on the constructed library using the double-end sequencing mode of Illumina sequencing platform.

value: Lung cancer organoid

value: lung

value: No treatment


title: P42-Treat

description: Library name: P01-077


title: SJRHB030476_X1_DYE0727_2D

description:
Library name: SJRHB030476_C2
2502289


title: P41-Treat

description: Library name: P01-076


description:
Library name: DE-12257-Yasmine-CH12
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 12 h post-infection  replica C
Yasmine-CH12_S43

value: 12 h post-infection


title: P40-Treat

description: Library name: P01-074

value: Esophagus tissue


title: P41-Baseline

description: Library name: P01-075


description:
Library name: DE-12256-Yasmine-CH10
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 10 h post-infection  replica C
Yasmine-CH10_S42

value: 10 h post-infection


title: SJRHB030476_X1_DYE0725_T0

description:
Library name: SJRHB030476_X1
2502287

value: Tumor


title: SJRHB030476_X1_DYE0726_3D

description:
Library name: SJRHB030476_C1
2502288


title: P40-Baseline

description: Library name: P01-073


title: P39-Treat

description: Library name: P01-072


description:
Library name: DE-12255-Yasmine-CH8
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 8 h post-infection  replica C
Yasmine-CH8_S41

value: 8 h post-infection


title: P38-Treat

description: Library name: P01-071


title: P37-Baseline

description: Library name: P01-067


description:
Library name: DE-12254-Yasmine-CH6
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 6 h post-infection  replica C
Yasmine-CH6_S40

value: 6 h post-infection


title: P36-Baseline

description: Library name: P01-066


title: SJRHB030705_X1_DYE0724_2D

description:
Library name: SJRHB030705_C2 Rep 1
2502286

value: Cells

value: RMS


title: SJRHB030705_X1_DYE0723_3D

description:
Library name: SJRHB030705_C1 Rep 1
2502285


title: P34-Treat

description: Library name: P01-064


description:
Library name: DE-12253-Yasmine-CH4
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 4 h post-infection  replica C
Yasmine-CH4_S39

value: Whole cells

value: 4 h post-infection


title: SJRHB030705_X1_DYE0722_T0

description:
Library name: SJRHB030705_X1
2502284


title: P33-Treat

description: Library name: P01-062


description:
Library name: DE-12252-Yasmine-CH2
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 2 h post-infection  replica C
Yasmine-CH2_S38

value: WT

value: 2 h post-infection


title: SJRHB015721_X1_DYE0721_2D

description:
Library name: SJRHB015721_C3
2502283


title: P34-Baseline

description: Library name: P01-063


title: P32-Baseline

description: Library name: P01-060


description:
Library name: DE-12251-Yasmine-CH0
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 30 min post-infection replica C
Yasmine-CH0_S37

value: Yasminevirus infected

value: 30 min post-infection


title: SJRHB015721_X1_DYE0720_3D

description:
Library name: SJRHB015721_C2
2502282


title: P30-Baseline

description: Library name: P01-058


description:
Library name: DE-12250-FadoliTnegB
Vermamoeba vermiformis mock infected control for Fadolivirus samples  replica B
FadoliTnegB_S36

value: mock infected

value: mock infected control


title: SJRHB015721_X1_DYE0719_T0

description:
Library name: SJRHB015721_X1
2502281


title: P29-Baseline

description: Library name: P01-057


title: P28-Treat

description: Library name: P01-056


title: SJRHB010468_X1_DYE0718_2D

description:
Library name: SJRHB010468_C2 Rep 1
2502280


title: P27-Treat

description: Library name: P01-054


title: P28-Baseline

description: Library name: P01-055


title: SJRHB010468_X1_DYE0717_3D

description:
Library name: SJRHB010468_C1 Rep 1
2502279


title: P26-Treat

description: Library name: P01-052


title: SJRHB010468_X1_DYE0716_T0

description:
Library name: SJRHB010468_X1
2502278


description:
Library name: DE-12246-Fadoli-BH8
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 8 h post-infection  replica B
Fadoli-BH8_S32

value: Fadolivirus infected


title: P26-Baseline

description: Library name: P01-051


title: P25-Treat

description: Library name: P01-050


title: P25-Baseline

description: Library name: P01-049


title: SJRHB071775_X1_DYE0714_VT

description:
Library name: SJRHB071775_C3
2502276

value: VT


title: P24-Baseline

description: Library name: P01-047

value: Esophagus tissue


title: P23-Baseline

description: Library name: P01-046


description:
Library name: DE-12244-Fadoli-BH4
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 4 h post-infection  replica B
Fadoli-BH4_S30


title: P22-Baseline

description: Library name: P01-045


title: SJRB012408_X1_DYE0712_T0

description:
Library name: SJRB012408_X1
2502272

value: RBL


description:
Library name: DE-12243-Fadoli-BH2
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 2 h post-infection  replica B
Fadoli-BH2_S29


title: SJRB071795_X1_DYE0710_T0

description:
Library name: SJRB071795_X1
2502270

value: Tumor


title: P21-Treat

description: Library name: P01-044


title: P21-Baseline

description: Library name: P01-043


description:
Library name: DE-12242-Fadoli-BH0
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 30 min post-infection  replica B
Fadoli-BH0_S28


title: SJRB071794_X1_DYE0709_3D

description:
Library name: SJRB071794_C1
2502269


title: P20-Treat

description: Library name: P01-042


title: P20-Baseline

description: Library name: P01-041


title: P19-Baseline

description: Library name: P01-040


title: SJRB071794_X1_DYE0708_T0

description:
Library name: SJRB071794_X1
2502268


title: P18-Baseline

description: Library name: P01-039


description:
Library name: DE-12241-YasmineTnegB
Vermamoeba vermiformis mock infected control for Yasminevirus samples  replica B
YasmineTnegB_S27


title: P17-Treat

description: Library name: P01-038


title: P35-Baseline

description: Library name: P01-065


description:
Library name: DE-12240-Yasmine-BH16
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 16 h post-infection  replica B
Yasmine-BH16_S26

value: 16 h post-infection


title: P33-Baseline

description: Library name: P01-061


title: SJRB030252_X1_DYE0707_VT

description:
Library name: SJRB030252_C2
2502267


title: P31-Baseline

description: Library name: P01-059


title: P17-Baseline

description: Library name: P01-037


title: P16-Baseline

description: Library name: P01-036


description:
Library name: DE-12239-Yasmine-BH12
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 12 h post-infection  replica B
Yasmine-BH12_S25

value: 12 h post-infection


title: P15-Treat

description: Library name: P01-035


title: SJRB030252_X1_DYE0706_3D

description:
Library name: SJRB030252_C1
2502266

value: Cells


title: P15-Baseline

description: Library name: P01-034


description:
Library name: DE-12238-Yasmine-BH10
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 10 h post-infection  replica B
Yasmine-BH10_S24

value: 10 h post-infection


description:
Library name: DE-12249-Fadoli-BH16
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 16 h post-infection  replica B
Fadoli-BH16_S35

value: Whole cells


title: SJRB030281_X1_DYE0704_2D

description:
Library name: SJRB030281_C1
2502264


title: P14-Baseline

description: Library name: P01-033


title: P27-Baseline

description: Library name: P01-053


description:
Library name: DE-12237-Yasmine-BH8
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 8 h post-infection  replica B
Yasmine-BH8_S23

value: 8 h post-infection


description:
Library name: DE-12247-Fadoli-BH10
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 10 h post-infection  replica B
Fadoli-BH10_S33

value: WT


description:
Library name: DE-12248-Fadoli-BH12
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 12 h post-infection  replica B
Fadoli-BH12_S34


title: P13-Treat

description: Library name: P01-032


title: SJRB030281_X1_DYE0702_T0

description:
Library name: SJRB030281_X1
2502262


title: P13-Baseline

description: Library name: P01-031


title: P12-Treat

description: Library name: P01-030


title: SJRB063840_X1_DYE0701_VT

description:
Library name: SJRB063840_C3
2502261


description:
Library name: DE-12236-Yasmine-BH6
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 6 h post-infection  replica B
Yasmine-BH6_S22

value: 6 h post-infection


title: P12-Baseline

description: Library name: P01-029


title: P11-Baseline

description: Library name: P01-028


title: SJRB063840_X1_DYE0700_2D

description:
Library name: SJRB063840_C2
2502260


description:
Library name: DE-12235-Yasmine-BH4
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 4 h post-infection  replica B
Yasmine-BH4_S21

value: Yasminevirus infected

value: 4 h post-infection


title: P10-Baseline

description: Library name: P01-025


title: P24-Treat

description: Library name: P01-048


title: SJRHB030680_X1_DYE0715_VT

description:
Library name: SJRHB030680_C5
2502277

value: RMS


title: P09-Treat

description: Library name: P01-022


description:
Library name: DE-12245-Fadoli-BH6
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 6 h post-infection  replica B
Fadoli-BH6_S31


description:
Library name: DE-12234-Yasmine-BH2
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 2 h post-infection  replica B
Yasmine-BH2_S20

value: 2 h post-infection


title: P09-Baseline

description: Library name: P01-021


title: SJRB063840_X1_DYE0699_3D

description:
Library name: SJRB063840_C1
2502259


description:
Library name: DE-12233-Yasmine-BH0
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 30 min post-infection replica B
Yasmine-BH0_S19

value: 30 min post-infection


title: P08-Treat

description: Library name: P01-019


title: SJRB063840_X1_DYE0698_T0

description:
Library name: SJRB063840_X1
2502258


title: P08-Baseline

description: Library name: P01-018


description:
Library name: DE-12232-FadoliTnegA
Vermamoeba vermiformis mock infected control for Fadolivirus samples  replica A
FadoliTnegA_S18

value: mock infected

value: mock infected control


title: P07-Treat

description: Library name: P01-017

value: Esophagus tissue


title: SJWLM031677_X2_DYE0697_2D

description:
Library name: SJWLM031677_C2
2502239


title: P07-Baseline

description: Library name: P01-016


description:
Library name: DE-12231-Fadoli-AH16
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 16 h post-infection  replica A
Fadoli-AH16_S17

value: Fadolivirus infected


title: P06-Baseline

description: Library name: P01-015


description:
Library name: DE-12230-Fadoli-AH12
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 12 h post-infection  replica A
Fadoli-AH12_S16


title: P05-Baseline

description: Library name: P01-013


title: SJWLM031677_X2_DYE0695_T0

description:
Library name: SJWLM031677_X2
2502237

value: Tumor


title: SJWLM031677_X2_DYE0696_3D

description:
Library name: SJWLM031677_C1
2502238


title: P04-Baseline

description: Library name: P01-011


description:
Library name: DE-12228-Fadoli-AH8
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 8 h post-infection  replica A
Fadoli-AH8_S14


title: P03-Treat

description: Library name: P01-010


title: P03-Baseline

description: Library name: P01-009


title: SJWLM030043_X1_DYE0693_T0

description:
Library name: SJWLM030043_X1
2502235


title: SJWLM031333_X1_DYE0692_2D

description:
Library name: SJWLM031333_C3
2502234


title: P02-Baseline

description: Library name: P01-008


description:
Library name: DE-12227-Fadoli-AH6
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 6 h post-infection  replica A
Fadoli-AH6_S13


description:
Library name: DE-12226-Fadoli-AH4
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 4 h post-infection  replica A
Fadoli-AH4_S12


title: SJWLM031333_X1_DYE0690_T0

description:
Library name: SJWLM031333_X1
2502232


title: SJOS030876_X1_DYE0689_2D

description:
Library name: SJOS030876_C3
2502190

value: OST


title: MOLM-13, PTBP1 IP, BB7 antibody

city: Philadelphia

first: Junwei

last: Shi

state: PA

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

description: Library name: MOLM13_PTBP1_BB7

library_source: other

data_processing:
*library strategy: eCLIP-seq
Adapter sequences were trimmed from all reads using Cutadapt (v3.5), and reads at least 18 bases were retained.
Trimmed reads were aligned to human Repbase29.11 (Bao et al., 2015), and then the unmapped reads were aligned to the human reference genome (GRCh38.p13), using STAR (v 2.7.10a).
PCR duplicates were removed with Picard Tools (v3.3.0).
The Yeo lab’s make_bigwig_files.py (v0.0.3) from the ENCODE eCLIP-seq Processing Pipeline was used to generate normalized strand-specific bigWig files.
Assembly: GRCh38.p13
Supplementary files format and content: The bigWig files contain strand-specific eCLIP-seq read coverage in the human genome GRCh38, normalized to read totals for comparison between samples and separated by strand.

molecule: other

source_name: blood

growth_protocol: Cells were grown in RPMI-1640 medium with 10% bovine calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
Cells were irradiated once with 400 mJ/cm² at 254 nm in a Stratalinker on ice. Cell pellets were collected by centrifugation at 500 × g for 5 min at 4°C and stored at −80°C until use. Pellets lysed in three pellet volumes of lysis buffer (50 mM Tris-HCl, pH 7.4; 150 mM NaCl; 1% NP-40; protease inhibitor cocktail) on ice. After 30 min, lysates were centrifuged at 17,000 × g for 30 min at 4°C, and the supernatant was collected. Fifty μL of protein G or protein A beads (prewashed 3× in wash buffer: 20 mM Tris-HCl, pH 7.6; 200 mM NaCl; 0.1% v/v NP-40; protease inhibitor cocktail) were added for pre-clearing at 4°C for 1 h with rotation. Samples were then centrifuged at 17,000 × g for 15 min at 4°C. The supernatant was treated with RNase T1 (final concentration 1 U/mL) for 15 min at 22°C with shaking, centrifuged at 14,000 rpm for 15 min at 4°C, filtered through a 0.45 μm filter, and 100 μL was saved as input. Antibody-conjugated beads [10 μg PTBP1 antibody (Millipore MABE986, clone BB7) with 50 μL protein G beads, or PTBP1 antibody (Abcam ab133734) with 50 μl protein A beads] were added, and samples were rotated for 4 h at 4°C. Beads were washed 3× with 1 mL wash buffer and resuspended in 100 μL wash buffer for a second RNase T1 treatment (10 U/μL) at room temperature for 8 min. Beads were washed 5× with 1 mL high-salt buffer (20 mM Tris-HCl, pH 7.6; 500 mM NaCl; 0.1% v/v NP-40; protease inhibitor cocktail), followed by a wash with PNK buffer without DTT (70 mM Tris-HCl, pH 7.4, and 10 mM MgCl₂). They were then resuspended in 50 μL dephosphorylation buffer (50 mM Tris-HCl, pH 7.9; 100 mM NaCl; 10 mM MgCl₂; 1 mM DTT; 0.5 U/μL calf intestinal alkaline phosphatase [NEB]) and incubated at 37°C for 10 min. Beads were washed 4× with PNK buffer without DTT, resuspended in 50 μL T4 PNK buffer (NEB B0201) with 2.5 μL T4 PNK enzyme (NEB M0201) and ATP, and incubated at 37°C for 30 min. They were washed 5× with 800 μL PNK buffer without DTT. One fortieth of the beads was saved and boiled for immunoblotting to confirm PTBP1–RNA complex pull-down and verify complex size. For elution, 50 μL 2× Laemmli buffer was added, and samples were boiled at 95°C for 5 min. Supernatants were run on a NuPAGE 4–12% Bis-Tris gel (Bio-Rad) at 160 V for 20 min. The gel region containing the complex was excised, mashed, and incubated with an equal volume of 2× proteinase K digestion buffer (100 mM Tris-HCl, pH 7.5; 150 mM NaCl; 12.5 mM EDTA; 2% w/v SDS) and water at 37°C for 30 min with shaking. For decrosslinking, proteinase K (20 mg/mL) and RNase inhibitor (10 μL) were added, and samples were incubated at 55°C for 1 h with shaking. RNA was extracted using phenol/chloroform and dissolved in 13 μL water.
The cDNA library was generated using the NEBNext Small RNA Library Prep Set for Illumina and sequenced on an Illumina NextSeq 550 platform with 75 bp single-end reads.

value: blood

value: acute myeloid leukemia

value: PTBP1 IP (Millipore MABE986, clone BB7)


title: MOLM-13, PTBP1 IP, Abcam antibody

description: Library name: MOLM13_PTBP1_Abcam

value: PTBP1 IP (Abcam ab133734)


title: MOLM-13, input

description: Library name: MOLM13_input


title: SJOS030876_X1_DYE0688_3D

description:
Library name: SJOS030876_C1
2502189

value: Cells


title: AML,PatientF29,CD3,PBMC,VDJ

city: Paris

first: Yannick

last: Simoni

address: 22 rue Mechain

country: France

institute: Institut Cochin

description: Library name: AML_PatientF29_CD3_PBMC_VDJ

data_processing:
FASTQ files for all modalities (GEX, ADT, TCR) were processed using the Cell Ranger (v7.0.1) multi pipeline.
Assembly: GRCh38-1.2.0
Supplementary files format and content: Cell Ranger output files: *barcodes.tsv.gz, *_features.tsv.gz, *_matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files: *filtered_contig_annotations.csv
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
Isolated blood or bone marrow T cells were isolated by FACS sorting from AML patients. Single-cell gene, surface protein and TCR repertoire analysis was performed using 10x Genomics technology. Sequencing libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index).
Libraries were performed according to the manufacter's instructions (Chromium Nex GEM Single Cell5' v2 (Dual Index) protocol, 10x Genomics).

value: Blood

value: CD3 T cells

tag: library type

value: TCR-seq


description:
Library name: DE-12225-Fadoli-AH2
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 2 h post-infection  replica A
Fadoli-AH2_S11

value: Whole cells

value: WT


description:
Library name: DE-12224-Fadoli-AH0
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 30 min post-infection  replica A
Fadoli-AH0_S10

value: 30 min post-infection


title: AML,PatientF29,CD3,PBMC,GEX

description: Library name: AML_PatientF29_CD3_PBMC_GEX

data_processing:
FASTQ files for all modalities (GEX, ADT, TCR) were processed using the Cell Ranger (v7.0.1) multi pipeline.
Assembly: GRCh38-1.2.0
Supplementary files format and content: Cell Ranger output files: *barcodes.tsv.gz, *_features.tsv.gz, *_matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files: *filtered_contig_annotations.csv
Library strategy: CITE-seq

value: mRNA


title: SJOS030876_X1_DYE0687_T0

description:
Library name: SJOS030876_X1
2502188


title: AML,PatientF29,CD3,BM,VDJ

description: Library name: AML_PatientF29_CD3_BM_VDJ

source_name: Bone marrow

value: Bone marrow


title: SJOS031478_X4_DYE0686_2D

description:
Library name: SJOS031478_C3
2502187


title: AML,PatientF29,CD3,BM,GEX

description: Library name: AML_PatientF29_CD3_BM_GEX


title: AML,PatientF29,CD3,BM,ADT

description: Library name: AML_PatientF29_CD3_BM_ADT

molecule: protein

value: ADT


description:
Library name: DE-12222-Yasmine-AH16
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 16 h post-infection  replica A
Yasmine-AH16_S8

value: Yasminevirus infected

value: 16 h post-infection


description:
Library name: DE-12221-Yasmine-AH12
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 12 h post-infection  replica A
Yasmine-AH12_S7

value: 12 h post-infection


title: AML,PatientG1,CD8,PBMC,GEX

description: Library name: AML_PatientG1_CD8_PBMC_GEX

value: CD8 T cells


title: AML,PatientG1,CD8,PBMC,ADT

description: Library name: AML_PatientG1_CD8_PBMC_ADT


title: AML,PatientG1,CD8,BM,VDJ

description: Library name: AML_PatientG1_CD8_BM_VDJ


title: SJNBL030721_X4_DYE0683_2D

description:
Library name: SJNBL030721_C10
2499135

value: NBL


description:
Library name: DE-12219-Yasmine-AH8
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 8 h post-infection  replica A
Yasmine-AH8_S5

value: 8 h post-infection


title: AML,PatientG1,CD8,BM,ADT

description: Library name: AML_PatientG1_CD8_BM_ADT


title: SJNBL030721_X4_DYE0682_3D

description:
Library name: SJNBL030721_C5 Rep 2
2499134


title: AML,PatientM12,CD8,BM,VDJ

description: Library name: AML_PatientM12_CD8_BM_VDJ


description:
Library name: DE-12218-Yasmine-AH6
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 6 h post-infection  replica A
Yasmine-AH6_S4

value: 6 h post-infection


title: AML,PatientM12,CD8,BM,GEX

description: Library name: AML_PatientM12_CD8_BM_GEX


title: SJNBL030721_X4_DYE0681_T0

description:
Library name: SJNBL030721_X4
2499133

value: Tumor


title: AML,PatientM12,CD8,BM,ADT

description: Library name: AML_PatientM12_CD8_BM_ADT


title: MI4

city: Pittsburgh

first: Partha

last: Dutta

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

description:
Library name: Sample 7
10x Genomics

data_processing:
Partek Flow (version 10.0.22.1204) software was used to analyze the single cell RNA seq data using the count matrix generated after the sequencing of the libraries.
The cells were filtered using these criteria: 12,000 read counts, 2,500 detected features, 8% mitochondrial reads, and 50% ribosomal counts.
The total UMI counts were normalized using Partek-recommended normalization method with CPM (counts per million) with Log2 transformation.
After the normalization, we filtered the data further by excluding the features where the gene expression values were <=1 in at least 99% of cells.
The graph based clustering analysis was performed by employing Louvain algorithm. To visualize the single cell data, we performed a t-distributed statistical neighbor embedding (tSNE) dimensional reduction and generated the plots.
Assembly: mm10
Supplementary files format and content: For the scRNA seq, the processed files include the count matrices.

source_name: Brain

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

value: Leukocytes

value: APOE4 KI

value: MI


title: SJNBL012407_X1_DYE0680_2D

description:
Library name: SJNBL012407_C2
2499132

value: Cells


title: MI3

description:
Library name: Sample 6
10x Genomics


description:
Library name: DE-12216-Yasmine-AH2
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 2 h post-infection  replica A
Yasmine-AH2_S2

value: Whole cells

value: WT

value: 2 h post-infection


title: MI2

description:
Library name: Sample 5
10x Genomics


title: SJNBL012407_X1_DYE0679_3D

description:
Library name: SJNBL012407_C1
2499131


title: MI1

description:
Library name: Sample 4
10x Genomics


description:
Library name: DE-12215-Yasmine-AH0
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 30 min post-infection replica A
Yasmine-AH0_S1

value: 30 min post-infection


title: Sham5

description:
Library name: Sample 3
10x Genomics

value: Sham surgery


title: SJNBL012407_X1_DYE0678_T0

description:
Library name: SJNBL012407_X1
2499130


title: Sham4

description:
Library name: Sample 2
10x Genomics


title: Sagittal section of whole brain of female surface fish

city: Columbia

first: Wesley

middle: C

last: Warren

state: MO

address: 1201 Rollins St.

department: Bond Life Sciences Center

institute: University of Missouri

description: Library name: surface_spatial

data_processing:
Reads were aligned to the AstMex3_surface reference genome and counts were collated into a count matrix using CellRanger v7.2.0
Assembly: AstMex3_surface
Supplementary files format and content: raw counts matrix
Library strategy: Spatial Transcriptomics

organism: Astyanax mexicanus

source_name: Whole brain

extract_protocol:
Nuclei were isolated from cryopreserved adult brain samples using the Singulator2 instrument per manufacturer’s protocols (S2 Genomics; Livermore, CA). After mechanical disruption, cell filter straining steps, and two washes at 250ul each, the cell nuclei were suspended in a nuclei isolation buffer (S2 Genomics; Livermore, CA), with all buffers containing 0.4U/ul Millipore RNAse inhibitor (SigmaAldrich). Nuclei were counted and evaluated for the amount of remaining cellular debris using the Cellometer instrument (Revvity; Waltham, MA).
Counted nuclei were prepared for microfluidic encapsulation on the 10X Chromium instrument (10x Genomics®, Pleasanton, CA) to nanoliter-scale Gel bead-in-EMulsions (GEMs). Single-nuclei libraries were generated using the GemCode Single-Cell Instrument, Single Cell 3′ Library and Gel Bead Kit v3, and Chip Kit (10x Genomics®, Pleasanton, CA) according to the manufacturer’s protocol. Before sequencing, every library was analyzed on a Bioanalyzer high sensitivity chip to ensure the expected cDNA fragment size distribution. The appropriate number of individually barcoded GEM libraries were pooled and sequenced on a NovaSeq 6000 instrument (Illumina) with 2x150bp length using these sequencing parameters: 26 bp read 1 – 8 bp index 1 (i7) – 98 bp read 2 with 200 cycles.

value: Whole brain

tag: Sex

value: female

tag: ecotype

value: Rio Choy surface


title: Sham2

description:
Library name: Sample 1
10x Genomics


title: SJNBL013762_X1_DYE0677_VT

description:
Library name: SJNBL013762_C4
2499129

value: VT

value: NBL


title: Bead+B39:B83s blank

description:
Library name: blanMrna
Beads blank
blanMrna_S55

organism: synthetic construct

value: blank


title: Whole brain of male surface fish, rep4

description: Library name: surface_M_S9

data_processing:
Reads were aligned to the AstMex3_surface reference genome and counts were collated into a count matrix using CellRanger v7.2.0
Assembly: AstMex3_surface
Supplementary files format and content: raw counts matrix

molecule: nuclear RNA

value: male


title: MC38, Lib138

city: Boston

first: Teng

last: Teng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

description:
Library name: ZL_Lib138_08152023a
EnCas12a immune evasion context discovery library infected MC38 engrafted in C57BL/6 or BALB/c-nude mice

library_source: genomic

data_processing:
In-house customized pipeline for mapping and counting for sgRNAs
Assembly: GrCh38
Supplementary files format and content: Tab-delimited text files include guide count and clone count values for each sample
Supplementary files format and content: gene_symbol: gene_name
Supplementary files format and content: guide: gRNA
Supplementary files format and content: sample_counts: number of counts for a specific guide and barcode
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: HCT116 and SiHa cells were grown in RPMI-1640 supplemented with 10% FBS. MC38 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
For in vitro CRISPR screen, gDNAs were extracted from collected HCT116 or SiHA cell pellets using HSM 2.0 (promega) with The ReliaPrep™ Large Volume HT gDNA Isolation System. For in vivo samples, tumors were harvested when mean tumor volume for a single group reached 1,000 mm3 for gDNA isolation and subsequent analysis by next-generation sequencing (NGS).
sgRNA sequences were PCR amplified with primers forward: F: 5′AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNCTTGTGGAAAGGACGAAACACCG-3′ (where N sequence are stagger squence range from 6nt to 13nt to create diversity), reverse: R: 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′ (where N sequence are 8nt index for demultiplexing) and purified with Kapa Pure Beads (Roche, KK8802)

treatment_protocol: For in vitro CRISPR screen, HCT116 (RRID:CVCL_0291) and SiHa (RRID:CVCL_0032) cells with stable Cas9 expression were infected with lentivirus encoding sgRNA against TMEM30A and selected by hygromycin. Cells were then infected with a genome-wide CRISPR KO library and sorted for Annexin V-high and Annexin V-low  populations to represent PS high and PS low population. For in vivo CRISPR screening, we constructed an immune evasion context discovery library consisting of 20 essential genes as controls for KO efficiency, 18 IO control genes, and 471 tumor suppressor genes and genes associated with immune evasion. MC38 cells were first infected with lentivirus encoding enCas12a and a blasticidin resistance gene (BSD) flanked by LoxP sites. Stable cells were then infected with a CRISPR KO library encoding a puromycin resistance gene and RFP flanked by Lox2272 sites and two gRNA sequences outside the floxed region. Cells were then infected with an insertion-deficient lentivirus encoding Cre recombinase and EGFP (IDV-Cre) and cultured for an additional two weeks before injected subcutaneously into the right flank of C57BL/6 (RRID:MGI:2159769) (n = 50) or BALB/c-nude (RRID:IMSR_RJ:BALB-C-NUDE) BALB/c-nude (n = 15) mice (1.0 x 106 cells per mouse). A sub-population of cells was also maintained in culture for collecting gDNA on the day of inoculation and on the day tumors were harvested. C57BL/6 (RRID:MGI:2159769) C57BL/6 mice were randomized for anti-PD-1 (n = 30) or IgG2a (n = 20) treatment when mean tumor volume reached 50 mm3, as described above. Tumors were harvested when mean tumor volume for a single group reached 1,000 mm3 for gDNA isolation and subsequent analysis by next-generation sequencing (NGS).

value: colon cancer cell line

tag: sample group


title: SJNBL046_X_DYE0676_VT

description:
Library name: SJNBL006105_C5
2499128

value: Tumor


title: Lacun3 STK11 KO biological replicate 4

city: Pamplona

first: Ruben

last: Pio

state: Navarra

address: Cima Building

department: Cancer Division

country: Spain

institute: Cima Universidad de Navarra

description:
Library name: S4_S8
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 KO; biological replicate 4.

data_processing:
FASTQ files were quality checked using FastQC v0.11.8.
Reads were aligned to the Mus musculus GRCm39 reference genome using STAR v2.7.9a with GENCODE mouse annotation vM33.
Gene-level counts were obtained with featureCounts v1.6.0.
Raw gene counts were normalized using edgeR and the voom function of limma.
Assembly: Mus musculus GRCm39; GENCODE mouse annotation vM33
Supplementary files format and content: Lacun3_STK11_RNAseq_raw_counts.tsv.gz: tab-delimited gzip-compressed matrix of raw gene-level counts. Rows are genes/features with Ensembl gene IDs and gene annotations; sample columns use library names.
Supplementary files format and content: Lacun3_STK11_RNAseq_voom_normalized_counts.tsv.gz: tab-delimited gzip-compressed matrix of limma-voom normalized expression values. Rows are genes/features with Ensembl gene IDs and gene annotations; sample columns use library names.

growth_protocol: Parental Lacun3 murine lung adenocarcinoma cells and CRISPR-generated Stk11-knockout Lacun3 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin in a humidified atmosphere containing 5% CO₂. Cells were routinely tested for Mycoplasma, and harvested during the logarithmic growth phase for RNA extraction.

extract_protocol:
RNA was extracted with the NucleoSpin RNA isolation kit (Macherey-Nagel), according to the manufacturer's instructions.
Libraries were prepared from 100 ng total RNA using the Illumina Stranded mRNA Prep kit at the Genomics Unit of Cima-Universidad de Navarra.Approximately 20-30 million paired-end reads (2 × 51 bp) were sequenced for each sample on an Illumina NextSeq 2000 platform.

treatment_protocol: No treatment was applied.

value: lung adenocarcinoma cell line

value: STK11 KO


title: Whole brain of male surface fish, rep3

description: Library name: surface_M_S13


description:
Library name: DE-12217-Yasmine-AH4
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 4 h post-infection  replica A
Yasmine-AH4_S3

value: Yasminevirus infected

value: 4 h post-infection


title: Lacun3 STK11 KO biological replicate 3

description:
Library name: S3_S7
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 KO; biological replicate 3.


title: SJNBL030721_X3_DYE0675_2D

description:
Library name: SJNBL030721_C9
2499127

value: Cells


title: Lacun3 STK11 KO biological replicate 2

description:
Library name: S2_S6
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 KO; biological replicate 2.


title: Whole brain of male cave fish, rep4

description: Library name: cave_M_P14

value: Pachon cave


title: Lacun3 STK11 KO biological replicate 1

description:
Library name: S1_S5
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 KO; biological replicate 1.


title: Lacun3 STK11 WT biological replicate 4

description:
Library name: C4_S4
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 WT; biological replicate 4.

value: STK11 WT


title: SJNBL030721_X3_DYE0674_3D

description:
Library name: SJNBL030721_C5 Rep 1
2499126


title: Whole brain of male cave fish, rep3

description: Library name: cave_M_P12


title: Lacun3 STK11 WT biological replicate 3

description:
Library name: C3_S3
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 WT; biological replicate 3.


title: SJNBL030721_X3_DYE0673_T0

description:
Library name: SJNBL013762_X3
2499125


title: Lacun3 STK11 WT biological replicate 2

description:
Library name: C2_S2
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 WT; biological replicate 2.


title: Whole brain of male surface fish, rep2

description: Library name: surface_M_S11


title: Lacun3 STK11 WT biological replicate 1

description:
Library name: C1_S1
Bulk RNA-seq of Lacun3 murine lung adenocarcinoma cells; STK11 WT; biological replicate 1.


title: SJEWS071783_X5_DYE0672_2D

description:
Library name: SJEWS071783_C6
2499070

value: EWS


title: Liver, CR, S19

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

country: Canada

institute: McMaster University

description:
Library name: Sample 19
FFPE Spatial transcriptome sequencing

data_processing:
The spatial transcriptomics (ST) data analysis in this paper includes raw data pre-processing and downstream data analysis. Raw data pre-processing consists of alignment of images, mapping, generation of gene-spot matrix and interpretation of outputs. Downstream data analysis includes quality control (QC), normalization, linear dimensional reduction, determination of principal components (PC), clustering, non-linear dimensional reduction (UMAP/t-SNE), identification of biomarkers, differentially expressed gene (DEG) analysis, spatially variable genes (SVGs), cell type annotations, integrative analysis, pseudobulk analysis, cell-cell communication, and metabolic activity analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5
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: scalefactors 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.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg: A registered and aligned tissue image used for spatial mapping
Supplementary files format and content: cytassist_image.tiff: A high-resolution image captured during the CytAssist workflow
Supplementary files format and content: spatial_enrichment.csv: A CSV file with spatial enrichment scores
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
Liver tissues were collected and fixed with 10% neutral-buffered formalin for 36–48 h. After fixation, the samples were immersed in a 70% alcohol solution. The liver tissues were then processed, paraffin-embedded, and sectioned. RNA quality of formalin-fixed & paraffin-embedded (FFPE) tissues was tested by TapeStation system with DV200 > 30%. Slides with 5 µm of tissue sections were processed with deparaffinization, H&E staining, imaging, decrosslinking, hybridization, ligation, probe extension, pre-amplification and probe-based library construction to generate gene expression libraries for each tissue for following sequencing. Images were taken using the Nikon 90i Eclipse upright microscope. RNA-seq was performed using the Illumina NextSeq 2000 (P2 Flow cell, 2 × 50 bp configuration) system. Sequence data from FFPE tissues were analyzed using the Space Ranger count pipeline from 10X genomics for raw data processing and quality control.
After confirming RNA quality of FFPE tissues (DV200 > 30%), slides with 5 µm of tissue sections were processed with deparaffinization, H&E staining, imaging and decrosslinking. Gene expression probes were then added to the tissues to target the whole transcriptome, enabling hybridization and ligation of each probe pair.  Probes were then released from the tissue upon Visium CytAssist Spatial Gene Expression Slide surface, which contains capture areas with barcoded spots that include oligonucleotides to capture gene expression probes. Visium CytAssist slides were removed from CytAssist for probe extension, pre-amplification and probe-based library construction to generate gene expression libraries for each tissue for following sequencing.

value: liver

value: WT

value: Caloric restriction


title: Whole brain of male cave fish, rep2

description: Library name: cave_M_P16

value: Whole brain


title: Liver, CR, S18

description:
Library name: Sample 18
FFPE Spatial transcriptome sequencing


title: SJEWS071783_X5_DYE0671_3D

description:
Library name: SJEWS071783_C3
2499069


title: Liver, GDF15, S11

description:
Library name: Sample 11
FFPE Spatial transcriptome sequencing


title: Whole brain of male cave fish, rep1

description: Library name: cave_M_P10


title: P05-Treat

description: Library name: P01-014

value: Esophagus tissue


title: Liver, GDF15, S10

description:
Library name: Sample 10
FFPE Spatial transcriptome sequencing


title: SJEWS071783_X5_DYE0670_T0

description:
Library name: SJEWS071783_X5
2499068


title: P04-Treat

description: Library name: P01-012


description:
Library name: DE-12229-Fadoli-AH10
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 10 h post-infection  replica A
Fadoli-AH10_S15

value: Whole cells

value: Fadolivirus infected

value: 10 h post-infection


title: Liver, PairFed, S35

description: Library name: Sample 35

data_processing:
We quantified the expression of transcripts using RNA-seq data through Salmon.
Salmon’s transcript-level quantifications DESeq2 was applied for detection of differentially expressed genes (DEG).
Assembly: mm10
Supplementary files format and content: a csv file include counts for all samples.

source_name: Liver

extract_protocol:
Tissues were homogenized and lysed in TRIzol reagent. After centrifuged, the supernatant (aqueous phase) was applied to the RNeasy kit (Qiagen, ID: 74106) for subsequent total RNA extraction and purification according to its protocols.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library kit following manufacturer's protocols.

treatment_protocol: Mice were placed on a MASH diet and housing condition (~29°C) at 8-weeks of age. Prior to treatment, mice were randomized and separated into different treatment groups matched on body weight and composition, and single-housed. Recombinant GDF15 (Novo Nordisk, NNC no. 0247-0000-0001, dissolved in synthetic buffer with 5 mM Acetate, 240 mM propylene glycol, and 0.007% polysorbate 20) was delivered by subcutaneous injection at 1-2 h post to light cycle in the morning (0700-0900) at 1 nmol/kg once daily. The individual dosage was calculated by body weight of one day before. Pair-fed animals received the same amount of food as ingested by the corresponding GDF15-treated groups the day before.

value: Liver

value: PairFed


title: Whole brain of female cave fish, rep5

description: Library name: cave_F_25.3

value: female


title: Liver, PairFed, S34

description: Library name: Sample 34


title: P01-Treat

description: Library name: P01-006

data_processing:
The Cell Ranger toolkit (version 6.1.0) provided by 10x Genomics was applied to aggregate raw data, filter low-quality reads, align reads to human reference genome (10X modified GRCh38, version 2020-A), assign cell barcodes, and generate the unique molecular identifier (UMI) matrix. A python-based toolkit, scanpy (version 1.9.1), was used for analyzing the scRNA-seq data. Specifically, the raw UMI matrixes of a total of 81 samples were firstly concatenated and then processed to filter out genes detected in less than 50 cells and cells with fewer than 500 genes or more than 50% counts of mitochondrial genes. For each sample, scrublet (version 0.2.3) was applied independently to identify doublets and remove, with an estimated doublet rate of 5%. The normalized expression matrix was calculated based on the raw UMI counts after normalizing total counts per cell (library size) and then scaled by 1e4 and log1p transformed.
Assembly: Human GRCh38
Supplementary files format and content: Expression h5ad file and cell annotation csv file


title: Liver, PairFed, S33

description: Library name: Sample 33


title: SJEWS030393_X1_DYE0669_2D

description:
Library name: SJEWS030393_C2
2499067


title: P01-Baseline

description: Library name: P01-005


title: Liver, PairFed, S32

description: Library name: Sample 32


title: Whole brain of male surface fish, rep1

description: Library name: surface_M_15.3

value: male

value: Rio Choy surface


title: SJEWS030393_X1_DYE0668_3D

description:
Library name: SJEWS030393_C1
2499066

value: Cells


title: Liver, PairFed, S31

description: Library name: Sample 31


title: Whole brain of female cave fish, rep4

description: Library name: cave_F_8.3

value: Pachon cave


title: Liver, GDF15, S30

description: Library name: Sample 30


title: SJEWS030393_X1_DYE0667_T0

description:
Library name: SJEWS030393_X1
2499065

value: Tumor


title: Liver, GDF15, S29

description: Library name: Sample 29


title: AML,PatientF29,CD3,PBMC,ADT

description: Library name: AML_PatientF29_CD3_PBMC_ADT

value: Blood

value: CD3 T cells

value: ADT


title: Whole brain of female surface fish, rep4

description: Library name: surface_F_7.3


title: Liver, GDF15, S27

description: Library name: Sample 27

value: WT


title: Liver, GDF15, S28

description: Library name: Sample 28


description:
Library name: DE-12223-YasmineTnegA
Vermamoeba vermiformis mock infected control for Yasminevirus samples  replica A
YasmineTnegA_S9

data_processing:
The Illumina integrate system was used to separate the bar-coded sequences and demultiplex paired end reads into FASTQ files.
The pre-trimmed RNA-seq data was validated with FastQC (v0.11.5) and MultiQC (v1.33). The data was re-trimmed using fastp (v0.21.0).
The paired-end reads were them mapped using HISAT2 to the combined fasta files consisting of the Yasminevirus GU-2018, Fadolivirus algeromassiliense and the Vermamoeba vermiformis CDC-19.
The subread algorithm featureCounts was used to generate gene-level quantification.
The data was then processed through the R (v4.5.1) package deseq2 to identify differentially expressed genes.
Assembly: combined fasta files consisting of the Yasminevirus GU-2018 (NCBI), Fadolivirus algeromassiliense (NCBI), and the Vermamoeba vermiformis CDC-19
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with coding regions of the genes.

value: mock infected

value: mock infected control


title: AML,PatientG1,CD8,PBMC,VDJ

description: Library name: AML_PatientG1_CD8_PBMC_VDJ

value: CD8 T cells

value: TCR-seq


title: SJEWS071785_X2_DYE0666_2D

description:
Library name: SJEWS071785_C4
2499064

value: EWS


title: Whole brain of female cave fish, rep3

description: Library name: cave_F_6.3

value: Whole brain


title: Liver, GDF15, S26

description: Library name: Sample 26

value: Liver


title: SJOS031478_X3_DYE0685_3D

description:
Library name: SJOS031478_C2
2502186

value: OST


title: SJEWS071785_X2_DYE0665_3D

description:
Library name: SJEWS071785_C2
2499063


title: Liver, Vehicle, S25

description: Library name: Sample 25

value: Vehicle


title: SJOS031478_X4_DYE0684_T0

description:
Library name: SJOS031478_X4
2502185


title: Whole brain of female surface fish, rep3

description: Library name: surface_F_5.3

value: female

value: Rio Choy surface


title: Liver, Vehicle, S24

description: Library name: Sample 24


title: SJEWS071785_X2_DYE0664_T0

description:
Library name: SJEWS071785_X2
2499062


description:
Library name: DE-12220-Yasmine-AH10
Vermamoeba vermiformis infected with Yasminevirus saudimassiliense A1/GU-2018 at 10 h post-infection  replica A
Yasmine-AH10_S6

value: Whole cells

value: Yasminevirus infected

value: 10 h post-infection


title: Whole brain of female cave fish, rep2

description: Library name: cave_F_4.3

value: Pachon cave


title: Liver, Vehicle, S22

description: Library name: Sample 22


title: Whole brain of female surface fish, rep2

description: Library name: surface_F_3.3


title: Liver, Vehicle, S21

description: Library name: Sample 21


title: Liver, Vehicle, S23

description: Library name: Sample 23


title: KPCY cells, Scr_biol rep 4

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Genes with less than 20 read counts in at least 2 samples were filtered out and differential gene expression analysis and processed using DESeq2 (v1.36.0) in R (version 4.2.1)
Differential expression analysis was performed using DESeq2, and genes with fold-change ≥ 1.5 and p-value < 0.05 were considered as differentially expressed
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw read counts for each sample

source_name: KPCY pancreatic cancer cells

extract_protocol:
0.3x106 were seeded in a six-well plate and 24 hours later, the cells were trypsinized, and RNA was isolated using Qiazol/chloroform, and miRNeasy kit followed by RNA Seq
Samples with a RIN of 7 and above were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 using the P3 reagents (100 cycle; Illumina) to generate paired-end reads (59 x 59 base pairs).

treatment_protocol:
KPCY Scr and miR-27a KD cells were grown in DMEM media containing L-Glutamine, 4.5g/L Glucose, without Sodium Pyruvate, and 10% Fetal Bovine Serum using a six well plate.
miR-27a  stable cells were generated by transducing miR-27a lentiviral vectors inhibiting miR-27a-3p and scrambled sequence. Transduced cells were treated with 2 µg/mL of puromycin for 7 days and the puromycin resistant cells were further grown passaged and used for future experiments.

value: KPCY pancreatic cancer cells

value: Male

value: Scrambled


title: SJEWS063834_X1_DYE0663_2D

description:
Library name: SJEWS063834_C2
2499061

value: Cells


title: AML,PatientG1,CD8,BM,GEX

description: Library name: AML_PatientG1_CD8_BM_GEX

value: Bone marrow

value: CD8 T cells

value: mRNA


title: SJEWS063834_X1_DYE0662_3D

description:
Library name: SJEWS063834_C1
2499060

value: EWS


title: Whole brain of female cave fish, rep1

description: Library name: cave_F_2.3

value: Whole brain


title: SJEWS063834_X1_DYE0661_T0

description:
Library name: SJEWS063834_X1
2499059

value: Tumor


title: KPCY cells, Scr_biol rep 2


title: KPCY cells, Scr_biol rep 1


title: KPCY cells, miR-27a KD_biol rep 4

value: miR-27a knockdown


title: Whole brain of female surface fish, rep1

description: Library name: surface_F_1.3

value: female


title: KPCY cells, miR-27a KD_biol rep 3


title: d32_04_08.1.RNA

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

description: Library name: HI_464

data_processing:
Demultiplexing, barcode processing, read counting, and aggregation were carried out using Cell Ranger Arc 2.0.2 with the mouse 2020-A transcriptome reference from 10X Genomics.
Read counts were analyzed using Seurat and Signac. Processed counts, cell type annotations, and other metadata were stored as a Seurat object in an RDS file.
Assembly: mm10
Supplementary files format and content: brain.so.rds: RDS file containing Seurat object with annotated single-cell data

source_name: cerebellum

extract_protocol:
Cerebellum from E14.5 litters were manually dissected in ice-cold PBS and flash-frozen in either a dry ice methanol bath (1 pair) or liquid nitrogen (3 pairs). Nuclei were prepared and processed through the 10X Multiome ATAC + Gene Expression protocol.
Sequencing libraries were constructed according to the 10X Genomics Multiome protocol.

value: cerebellum

tag: developmental stage

tag: mouse strain

value: FVB

value: WT

value: Female

tag: mouse id


title: KPCY cells, miR-27a KD_biol rep 2


title: KPCY cells, miR-27a KD_biol rep 1


title: d32_04_05.1.RNA

description: Library name: HI_462

value: Mut


title: FAPs, miR-27a-KD_biol rep 3

source_name: Hindlimb muscle

growth_protocol: KPCYScr and miR-27aKD cell lines was grown in DMEM media containing L-Glutamine, 4.5g/L Glucose, without Sodium Pyruvate, and 10% Fetal Bovine Serum.

extract_protocol:
FAPs were sorted using an Influx cell sorter (Becton Dickinson) with the following gating strategy: CD31-/ CD45-/ α7-integrin-/ PI-/ SCA-1+/ Hoechst 33342+. RNA of sorted FAPs was isolated using a combination of Qiazol/chloroform, and miRNeasy kit.
Samples with a RIN of 7 and above were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 using the P3 reagents (100 cycle; Illumina) to generate paired-end reads (59 x 59 base pairs).

treatment_protocol: miR-27a stable cell line was generated by transducing KPCY cell line with miR-27a lentiviral vector inhibiting the expression of miR-27a-3p. Similarly, KPCY control stable cell line was generated by transducing KPCY cell line with lentiviral vector expressing scrambled sequence. Transduced cells were treated with 2 µg/mL of puromycin for 7 days and the puromycin-resistant cells were further passaged and used for future experiments. 2 million cells in 50uL were injected into the pancreas. Control mice received sham surgery.

value: Hindlimb muscle

value: Freshly sorted FAPs

tag: strain

value: Orthotopic implantation of KPCY miR-27a KD cells


title: SJRHB013757_X2_DYE8737_2D

description:
Library name: SJRHB013757_C1 Rep 2
2364121

value: Cells

value: RMS


title: d32_04_04.1.RNA

description: Library name: HI_460

value: Male


title: FAPs, miR-27a-KD_biol rep 2


title: FAPs, miR-27a-KD_biol rep 1


title: d32_04_01.1.RNA

description: Library name: HI_458


title: FAPs, KPC Scr_biol rep 3

value: Orthotopic implantation of KPCY scrambled cells


title: FAPs, KPC Scr_biol rep 2


title: SJRHB013757_X2_DYE8735_T0

description:
Library name: SJRHB013757_X2
2364119


title: FAPs, KPC Scr_biol rep 1


title: mj2_02_02.1.RNA

description: Library name: HI_456

value: BKS


title: FAPs, Control-biol rep 2

value: Sham treatment


title: FAPs, Control-biol rep 1


title: mj2_02_06.1.RNA

description: Library name: HI_454


title: SJRHB030680_X1_DYE8734_T0

description:
Library name: SJRHB030680_X1
2364118

value: Tumor


title: SJRHB013758_X2_DYE8733_T0

description:
Library name: SJRHB013758_X2
2364117


title: FAPs, KPC- Day 14 biol rep 3

description:
234E6
FAPs_Day_14_raw_counts.txt

growth_protocol: KPCY cell line was grown in DMEM media containing L-Glutamine, 4.5g/L Glucose, without Sodium Pyruvate, and 10% Fetal Bovine Serum.

treatment_protocol: 2 million cells in 50uL were injected into the pancreas. Control mice received sham surgery

value: Orthotopic implantation of KPCY cells

value: Day 14


title: mj2_02_03.1.RNA

description: Library name: HI_452

value: cerebellum


title: FAPs, KPC- Day 14 biol rep 2

description:
234E4
FAPs_Day_14_raw_counts.txt


title: SJRHB013758_X1_DYE8732_T0

description:
Library name: SJRHB013758_X1
2364116


title: FAPs, KPC- Day 14 biol rep 1

description:
234E3
FAPs_Day_14_raw_counts.txt


title: FAPs, Control-Day 14_biol rep 3

description:
241A8
FAPs_Day_14_raw_counts.txt


title: mj2_12_05.1.RNA

description: Library name: HI_450


title: FAPs, Control-Day 14_biol rep 2

description:
241A6
FAPs_Day_14_raw_counts.txt


title: mj2_12_03.1.RNA

description: Library name: HI_448


title: FAPs, Control-Day 14_biol rep 1

description:
241A7
FAPs_Day_14_raw_counts.txt


title: Control rep2

status: Public on Aug 11 2026

first: Wang

last: Lin

state: Shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai, China

department: College of Life Science

institute: Fudan University

description:
Library name: en/+_2
Column name in processed files:en_w1118-2

data_processing:
The resulting cDNA library was sequenced using Illumina Novaseq6000
Reads were further filtered by fastp (version 0.18.0)
paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release109
Supplementary files format and content: csv files include FPKM for each sample
Supplementary files format and content: csv files include diff gene expression(NAT10-RNAi vs Control)
Supplementary files format and content: csv files include diff gene expression(NAT10-RNAi Xrp1-RNAi vs Control)

organism: Drosophila melanogaster

source_name: Wing disc

growth_protocol: All Drosophila stocks were maintained on standard cornmeal–yeast–agar–syrup food at 25 °C.

extract_protocol:
Total RNA from 100 dissected wing disc was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer(Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beadsThen the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).

treatment_protocol: Wing discs were dissected from third instar larvae of the indicated genotypes in ice-cold PBS.

value: Wing disc

value: epithelial cells


title: FAPs, KPC- Day 21 biol rep 3

description:
273A2
FAPs_Day_21_raw_counts.txt

value: Day 21


title: FAPs, KPC- Day 21 biol rep 2

description:
276A3
FAPs_Day_21_raw_counts.txt


title: d32_04_08.1.ATAC

description: Library name: HI_451

library_source: genomic single cell

value: FVB

value: WT

value: Female


title: PL1 cell line REP 1

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description: Library name: PL1A

data_processing:
Raw read quality was assessed using FASTQC. Reads were aligned to the Mus musculus reference genome (GRCm38, GENCODE M25) using the STAR aligner with default settings. Gene-level quantification (raw counts, transcripts per million [TPM], and fragments per kilobase million [FPKM]) was performed using the RSEM algorithm. Differential gene expression analysis was conducted using the DESeq2.
Assembly: GRCm38, Genome Reference Consortium Mouse Build 38 Organism
Supplementary files format and content: text file contains trancripts per million for each sample

source_name: mouse LUSC

extract_protocol:
Total RNA was extracted from PL and PLA murine cell lines using the RNeasy Plus Universal Mini Kit (QIAGEN) according to the manufacturer’s instructions.
cDNA synthesis was performed using the SMARTer PCR cDNA Synthesis Kit (Clontech), followed by library preparation with the Nextera XT DNA Library Preparation Kit (Illumina), following standard protocols

value: mouse LUSC


title: d32_04_05.1.ATAC

description: Library name: HI_449

value: Mut


title: FAPs, Control-Day 21_biol rep 3

description:
265B9
FAPs_Day_21_raw_counts.txt

value: Hindlimb muscle

value: Freshly sorted FAPs


title: SJRHB031320_X1_DYE8559_VT

description:
Library name: SJRHB031320_C5
2355610

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

value: VT

value: RMS


title: d32_04_04.1.ATAC

description: Library name: HI_447

value: Male


title: FAPs, Control-Day 21_biol rep 2

description:
265B7
FAPs_Day_21_raw_counts.txt

value: Sham treatment


title: FAPs, Control-Day 21_biol rep 1

description:
265B5
FAPs_Day_21_raw_counts.txt


title: PLA cell line REP 2

description: Library name: HHPLAB


title: FAPs, KPC- Day 26_biol rep 3

description:
226D3
FAPs_Day_26_raw_counts.txt

value: Orthotopic implantation of KPCY cells

value: Day 26


title: d32_04_01.1.ATAC

description: Library name: HI_445

value: cerebellum


title: Primary human keloid fibroblasts, ADSC-mitochondria treatment 24 h, rep3

first: Wenjing

address: No. 33 Ba-Da-Chu Road

department: Department of Plastic and Reconstructive Surgery

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: mitoKF3

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: Tab‑delimited text file include gene‑count values for each sample.

source_name: Primary human keloid fibroblasts isolated from human keloid tissue

extract_protocol:
1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into a tissue grinding tube (tissue ≤ 30 mg, cells ≤ 1×10⁷). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the sample using a rotor–stator homogenizer, and incubate the lysate at room temperature for 5 min. 1.1.3 Centrifuge at 12,000× g for 3 min at room temperature, then transfer the supernatant onto the AllPrep DNA spin column. 1.1.4 Centrifuge at 12,000× g for 30 s at room temperature. Retain the flow-through in the collection tube for subsequent RNA purification. 1.1.5 Transfer the AllPrep DNA spin column into a new collection tube for DNA purification.  1.2 DNA Purification 1.2.1 Add 500 μL Buffer AW1 to the AllPrep DNA spin column, centrifuge at 10,000× g for 30 s, and discard the flow-through. 1.2.2 Add 500 μL Buffer AW2 to the AllPrep DNA spin column, centrifuge at 10,000× g for 30 s, and discard the flow-through. 1.2.3 Perform a dry spin at 16,000× g for 2 min. Transfer the AllPrep DNA spin column into a 1.5 mL microcentrifuge tube. 1.2.4 Add 50 μL Buffer EB onto the column membrane, and incubate at room temperature for 1 min. 1.2.5 Centrifuge at 16,000× g for 2 min to elute DNA.  1.3 RNA Purification 1.3.1 Add an equal volume of 70% ethanol to the flow-through collected in step 1.1.4 and mix thoroughly by pipetting. 1.3.2 Transfer up to 700 μL of the mixture onto an RNeasy spin column placed in a 2 mL collection tube. 1.3.3 Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.4 Add 700 μL Buffer RW1 to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.5 Add 500 μL Buffer RPE to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.6 Add another 500 μL Buffer RPE to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.7 Centrifuge at 16,000× g for 2 min to dry the column membrane, then transfer the RNeasy spin column into a 1.5 mL microcentrifuge tube. 1.3.8 Add 35 μL RNase-free water onto the column membrane and incubate at room temperature for 1 min. 1.3.9 Centrifuge at 16,000× g for 2 min at room temperature to elute purified RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: ADSC-mitochondria treatment 24 h


title: FAPs, KPC- Day 26_biol rep 2

description:
227C4
FAPs_Day_26_raw_counts.txt


title: SJRHB063823_X1_DYE8557_VT

description:
Library name: SJRHB063823_C3
2355608

value: Tumor


title: FAPs, Control- Day 26_biol rep 4

description:
235A4
FAPs_Day_26_raw_counts.txt


title: mj2_02_02.1.ATAC

description: Library name: HI_443

value: BKS


title: SJRHB046156_X1_DYE8556_VT

description:
Library name: SJRHB046156_C6
2355607


title: FAPs, Control- Day 26_biol rep 2

description:
227B5
FAPs_Day_26_raw_counts.txt


title: SJRHB013759_X15_DYE8555_VT

description:
Library name: SJRHB013759_C14
2355606


title: FAPs, Control- Day 26_biol rep 1

description:
227B4
FAPs_Day_26_raw_counts.txt


title: FAPs, Control- Day 26_biol rep 3

description:
227B6
FAPs_Day_26_raw_counts.txt


title: mj2_02_03.1.ATAC

description: Library name: HI_539


title: Quadriceps Muscle, KPCY

data_processing:
Demultiplexed FASTQ reads were aligned to the mouse reference genome, mm10 (GRCm38.p5, primary assembly) using the 10X Genomics Cellranger v6.0.1. Default and recommended parameters were adopted. The resulting gene-barcode matrices were processed and analyzed in Seurat (Satija Lab, v5.0.1).
Quality control metrics including the number of genes expressed, total unique molecular identifier, and proportion of mitochondrial transcripts were tailored to each dataset to remove cells of poor quality. Data was then processed using principal component analysis, Louvain clustering, and dimensionality reduction with UMAP. Differential gene expression using the Wilcoxon rank sum test was performed on filtered and normalized counts.
Assembly: mm10
Supplementary files format and content: HDF5 file containing gene count matrices

source_name: Quadriceps Muscle

extract_protocol:
Quadriceps muscle was isolated, immediately minced and transferred to the gentleMACS C Tube containing ice-cold lysis buffer, RNaseOUT, Recombinant Ribonuclease Inhibitor, 1mM DTT in Nuclei Extraction Buffer. The tissue was dissociated by using the 4C_nuclei_1 on the gentleMACS dissociator. The nuclei suspension was passed through the MACS 70 μm SmartStrainer, followed by washing the MACS SmartStrainer with 2 mL of 2% Bovine serum albumin. The nuclei suspension was centrifuged at 500×g at 4 °C for 5 minutes and the supernatant was aspirated. Nuclei pellet was resuspended in 2mL of BSA and the nuclei suspension was applied to a 30 μm MACS SmartStrainer followed by the addition of DAPI. The sorted DAPI+ cells were and the supernatant was aspirated followed by resuspending the pellet.
Nuclei were delivered into a Chromium Controller (10X Genomics), captured and libraried with the Chromium single cell 3’ reagent kit v3 (10X Genomics) as per the manufacturer's protocol. Sample integrity was assessed on the Agilent Bioanalyzer 2100 system). cDNA libraries were sequenced on Illumina Nextseq 2000 using the P3 100-cycles kits (59 x 59 base pair reads) to a minimum depth of 20,000 mean reads per nucleus.
snRNA-Seq

value: Quadriceps Muscle

value: Freshly isolated nuclei

value: Orthotopic implantation of 2million KPCY cells


title: SJRHB013758_X2_DYE8553_VT

description:
Library name: SJRHB013758_C9
2355604

source_name: Tumor


title: mj2_12_05.1.ATAC

description: Library name: HI_537

value: WT


title: mj2_02_06.1.ATAC

description: Library name: HI_541

value: Female


title: Quadriceps Muscle, Control

value: Sham surgery


title: iBUC_21pl9

city: Rehovot

first: Sharon

last: Schlesinger

address: Herzl 229

department: Animal Science

country: Israel

institute: Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem

description: Library name: SV40_FBS-4

data_processing:
Sequence reads were trimmed for adaptor and polyA using Cutadapt
Trimmed sequence reads were mapped to Bos_taurus.ARS-UCD1.2 genome using STAR
Read count extraction to fatures using HTSeq
Normalization of the counts and differential expression analysis using DESeq
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: raw_counts_wj_sv40.xlsx
Library strategy: Bulk MARS-seq

organism: Bos taurus

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in low glucose Dulbecco's Modified Eagle's Medium, containing 10% Fetal Bovine Serum (FBS), penicillin-streptomycin solution 1% , Glutamine 1%, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted via PureLink RNA Minikit
Library preparation was done by Weizmann Institute, Rehovot. Sequencing Libraries were prepared using Bulk MARS-Seq. SR reads were sequenced on 1 lane(s) of an Illumina NovaSeq Sp (100 cycles). The output was ~25 million reads per sample.

treatment_protocol: cells were immortalized by transient transfection of a plasmid carrying the SV40 large T antigen for the WJ-SV40 line

value: umbilical cord

value: Immortalized SV-40

value: mesenchymal stem cells

tag: breed

value: Holstein

value: immortalized cells, 21 days culturing


title: mj2_12_03.1.ATAC

description: Library name: HI_535

value: Mut

value: Male


title: NIH/3T3 cells KrasWT_1

city: Houston

first: Ronald

middle: J

last: Parchem

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Library name: WT1
mRNA-seq
NIH3T3_KrasWT_mRNA_Dcp1aOE_normalizedcounts.csv
WT1

data_processing:
Reads were trimmed with cutadapt, and aligned to mm10 with STAR
Assembly: mm39
Supplementary files format and content: Common-separated values of normalized counts

source_name: pancreas

growth_protocol: 10% FBS+1xglutamax in DMEM/F12

extract_protocol:
Trizol total RNA extraction
illumina Truseq stranded mRNA

value: pancreas

tag: cell line

value: fibroblast

value: KrasWT


title: iBUC_21pl6

description: Library name: SV40_FBS-1

tag: cell type


title: SJRHB000026_X2_DYE8551_VT

description:
Library name: SJRHB000026_C8
2355602

value: Tumor

value: VT

value: RMS


title: iBUC_21pl5

description: Library name: SV40_AM-5


title: SJRHB010928_X1_DYE8550_VT

description:
Library name: SJRHB010928_C4
2355601


title: Multiome, Col-0 72h seedling, 4h ethylene, rep2, ATAC

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: 250526_multiATAC_Ath_3do_seedling_4ET_2_1_10xATAC

data_processing:
Cell by gene matrices and fragment files were generated with Cellranger-arc v2.0.2
Assembly: TAIR10 genome; Araport 11 transcriptome
Supplementary files format and content: harmony.rds, Seurat object that contains the snRNA-seq dataset of whole seedlings
Supplementary files format and content: apical_clusters.rds, Seurat object that contains cells that compose the apical seedling
Supplementary files format and content: spatial_multiome_imputed_250825.rds, Seurat object that contains cells related to the spatial multi-modal integration
Supplementary files format and content: GA_subclust26_multiome_imputed_250825.rds, Seurat object that contains the AHR (cluster 26) cells

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis seedlings were grown at 23C in complete darkness for 72h prior to harvest

extract_protocol:
Nuclei were extracted as described in (47), with slight modifications. Plants were grown as described previously, and nuclei were immediately extracted from air-grown seedlings following 28h, 48h, and 72h of growth and 72 h-old seedlings following 4h ET treatment in a green room. Purified nuclei were used as input for the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit.
Sequencing libraries were constructed following the manufacturer’s instructions and were sequenced with the Illumina NovaSeq X.

treatment_protocol: Control plants were treated with Zero grade air in sealed chambers at a rate of 30mL / min. Treated plants were exposed to 10 ppm ethylene gas at a flow rate of 30mL / min for the indicated treatment lengths.

value: Seedling

tag: genotype

value: 4h ethylene

tag: developmental timepoint


title: iBUC_21pl4

description: Library name: SV40_AM-4

tag: treatment


title: Multiome, Col-0 28h seedling, control, rep1, ATAC

description: Library name: 24240206_ethylene_Ath_28h_seedling_air_1_1_multi_ATAC

value: Control


title: iBUC_21pl2

description: Library name: SV40_AM-2


title: Multiome, Col-0 72h seedling, control, rep3, ATAC

description: Library name: 241001_ethylene_Ath_72h_seedling_air_3_1_multi_ATAC


title: SJRHB010927_X1_DYE8549_VT

first: Michael

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
Library name: SJRHB010927_C3
2355600

tag: batch


title: iBUC_21pl1

description: Library name: SV40_AM-1

tag: tissue


title: SJRHB000026_X1_DYE8548_VT

description:
Library name: SJRHB000026_C7
2355599


title: Multiome, Col-0 72h seedling, control, rep2, ATAC

description: Library name: 241001_ethylene_Ath_72h_seedling_air_2_1_multi_ATAC


title: iBUC_165pl4

description: Library name: SV-40_2D-4

value: immortalized cells, 165 days culturing


title: iBUC_165pl3

description: Library name: SV-40_2D-3

value: umbilical cord


title: SJRHB015720_X1_DY8443_VT

description:
Library name: SJRHB015720_C3
2344270


title: SJRHB012_Z_DY8442_VT

description:
Library name: SJRHB000912_C8
2344269


title: iBUC_165pl1

description: Library name: SV-40_2D-1

value: Immortalized SV-40


title: Multiome, Col-0 72h seedling, 4h ethylene, rep1, ATAC

description: Library name: 220422_multiATAC_Ath_3do_seedling_4ET_1_1


title: pBUC_50lp6

description: Library name: P18_WJ_F

value: primary cell culture

value: mesenchymal stem cells

value: no treatment, 50 days culturing


title: pBUC_50lp5

description: Library name: P18_BUC

value: Holstein


title: Multiome, Col-0 72h seedling, 0h control, rep1, ATAC

description: Library name: 220422_multiATAC_Ath_3do_seedling_0ET_1_1

value: 0h control


title: pBUC_50lp4

description: Library name: P15_WJ


title: pBUC_50lp3

description: Library name: P15_BUC


title: SJRHB012_Z_DY8440_3D

description:
Library name: SJRHB000912_C2 Rep 2
2344267

source_name: Cells

value: Cells


title: Multiome, Col-0 72h seedling, 4h ethylene, rep2, RNA

description: Library name: 250526_multiRNA_Ath_3do_seedling_4ET_2_1_10xRNA