title: COJO-PBMC-TIL-2-D14

description: Library name: S11732Nr52


title: KS_B1

status: Public on Dec 04 2025

type: SRA

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

country: USA

institute: NIH / National Cancer Institute

description:
Library name: 7630-JMZ-S1-A
FFPE from Patient

library_source: transcriptomic

data_processing:
The raw original FASTQ files were generated through 10X Visium pipeline with the respective TIFF image file using v1 and v2 probe with 5 KSHV spiked in the probes respectively.
A combined reference of HG38 with adding Human herpesvirus 8 strain GK18 (NC_009333) (spaceranger_hg38_kshv_refrence.gz) and a probe set V2 (Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K.csv)
Processed FASTQ files were aligned to a custom reference with KSHV genome (NC_009333.1) added using SpaceRanger “count” module (version 3.0.0) (supplementary files: spaceranger_hg38_kshv_refrence.gz, Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K2.csv or Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K.csv).
Assembly: spaceranger_hg38_kshv_refrence
Supplementary files format and content: positions.csv.gz, positions_list.csv.gz: list of barcodes and their coordinations
Supplementary files format and content: feature.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: *.tif.gz: Tiff file for the tissue
Supplementary files format and content: *.json.gz: Spots information
Supplementary files format and content: *.png.gz: Spots information
Library strategy: Spatial Transcriptomics

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: cutaneous KS tumor

extract_protocol:
FFPE treated samples were deparaffinized with investigator placed sections, H&E stained, imaged and decrosslinked.
The tissue was permeabilized and 10X Genomics human transcriptome V1 probes were hybridized to the mRNA overnight for KS_A1, KS_A2, and KS_A3. For KS_B1, KS_B2, and KS_B3 and KS_B4 the same process was performed with V2 and spiked KSHV genes (listed in Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A_K2.csv).  The probes were ligated, released from the tissue, captured on the spatially barcoded spots and subjected to extension followed by denaturation per manufacturer protocol.

tag: tissue

value: cutaneous KS tumor


title: COJO-PBMC-TIL-2-D1

city: Solna

first: Lucas

last: Arruda

address: Nanna Svartz väg  4

country: Sweden

institute: CuraCell AB

description: Library name: S11732Nr50

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014). Quality trimming of the reads has not been performed. The FASTQ files were downsampled to 2 million read pairs before TCR analysis. Overlapping paired reads were merged into single reads before reconstruction of the CDR3β regions using NGmerge (Gaspar 2018). Only read pairs that could be successfully merged into a single read were kept for further analysis. Reconstruction of T cell receptor sequences was performed using RTCR (Gerritsen et al. 2016).
Assembly: hg38
Supplementary files format and content: csv files contain the assembled CDR3 sequences

molecule: total RNA

source_name: Blood

extract_protocol:
RNA was extracted using MagMax (Thermo Fisher)
AmpliSeq™ for Illumina® TCR beta-SR Panel (Illumina)

value: Blood

tag: cell line

value: PBMC

tag: cell type


title: MYEOV_KD#2_S3

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Sample 9

data_processing:
Adaptor and low-quality sequences were trimmed from the raw reads and the trimmed reads were aligned to the reference genome using the STAR program (version 2.6.1d). Differential expression analyses were performed by the DESeq2 R package (version 1.28.0).
Assembly: hg38
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

source_name: Cultured corneal epithelial cells

extract_protocol:
Human donor corneas were obtained from eye banks. The central cornea was removed by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. Dissociated limbal epithelial cells were cultured and treated with siRNAs (Control, MYEOV knockdown #1, and MYEOV knockdown #2).  Transfection was repeated on day 2 and day 4 and the cells were harvested on day 7 for RNA extraction.
After the removal of rRNA, approximately 500 ng of total RNA underwent library preparation with the Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research). RNA-seq libraries were sequenced on an Illumina NovaSeq to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.

value: Cultured corneal epithelial cells

value: In vitro human corneal epithelial cells

tag: treatment

value: Sample 3, MYEOV knockdown #2


title: COJO-TIL-2

description: Library name: S11732Nr49

source_name: TIL

value: TIL

value: T-cells


title: COJO-PBMC-TIL-1-M1

description: Library name: S11732Nr48


title: MLO_DJ1KO_organoid_1_replicate_6

type: other

city: Singapore

first: Matas

last: Vitkauskas

address: 60 Biopolis St.

department: Genome Institute of Singapore

country: Singapore

institute: A*star research entities

description:
60
DJ-1 KO

hyb_protocol: Following cryosectioning, sections were fixed for 1 min with ice-cold 4% PFA then 3:1 MeOH:acetic acid for 5 min, with 3x5 min washes with cold PBS in between. Air-dried coverslips were stored at −20°C. Coverslips were thawed and permeabilized with 70% EtOH at 4°C for 48 h, and incubated with wash buffer for 2 h in a 47°C incubator, before 48 h incubation at 47°C with 75–100 uM of encoding probe library. Before imaging, coverslips were washed twice with wash buffer for 15 min at 47°C, stained with DAPI, then washed twice with 2X saline-sodium citrate buffer.

scan_protocol: Imaging was performed on a commercial platform using a custom-built microscope.

data_processing:
Images of individual hybridization rounds were merged by z-stack and stitched to get joint X-Y coordinates per organoid section. RNA spots were decoded from the codebook using logic outlined in section “design and construction of the MERFISH encoding probes”. Cell segmentation of DAPI+ images staining for cell nuclei were segmented using CellPose v2.0 (Pachitariu & Stringer, 2022). The obtained .png cell mask and .hdf5 spot files were then put into a custom spot assignment script that assigns spots to cells within the cell area from the cell mask. Spots assigned to unsegmented areas were filtered out.
total counts of RNA spots per sample for each gene in the MERFISH panel.

molecule: other

source_name: human midbrain-like organoids

growth_protocol: hMLOs were generated as previously published (Jo, et al., 2016) (Jo, et al., 2021). In brief, TrypLE-Express-dissociated hPSCs were seeded into a V-bottom 96-well culture plate (Sumitomo Bakelite) in neuronal induction media with the ROCK inhibitor thiazovivin, which was removed after 24 h. Neuronal induction medium, used for the first three days, contained DMEM/F12:Neurobasal (1:1), N2 supplement (1:100), B27 without vitamin A (1:50), GlutaMAX (1%), minimum essential media-nonessential amino acid (1%), and β-mercaptoethanol (0.1%) (all Invitrogen) supplemented with 1 μg/ml heparin (Sigma-Aldrich), 10 μM SB431542 (Stemgent), 200 ng/ml Noggin (Prospec), and 0.8 μM CHIR99021 (Reagents Direct). On day 3, 100 ng/ml SHH-C25II and 100 ng/ml FGF8 (both R&D Systems), along with 0.5 μM purmorphamine (Stemgent), were added for midbrain patterning. On day 7, media was completely removed and organoids were embedded in reduced growth factor Matrigel and left to solidify in a 37°C incubator for 30 min, then grown in tissue growth induction medium containing Neurobasal, 1:100 N2 supplement, 1:50 B27 without vitamin A, 1% GlutaMAX, 1% minimum essential media-nonessential amino acid, and 0.1% β-mercaptoethanol supplemented with 2.5 μg/ml insulin (Sigma-Aldrich), 200 ng/ml laminin (Sigma-Aldrich), 100 ng/ml SHH-C25II, and 100 ng/ml FGF8. On day 8, hMLOs were transferred using a wide-bore pipette tip into low-attachment 6-well-plates (Costar) in final differentiation media, consisting of Neurobasal medium, N2 supplement (1:100), B27 without vitamin A (1:50), GlutaMAX (1%), minimum essential media-nonessential amino acid (1%), β-mercaptoethanol (0.1%), 10ng/ml BDNF (Peprotech), 10 ng/ml GDNF (Peprotech), 100 μM ascorbic acid (Sigma-Aldrich), and 125 μM db-cAMP (Sigma-Aldrich), and were cultured on orbital shakers for maintenance.

extract_protocol: Following manufacturer’s protocol, 50 units of papain enzyme (Worthington) was activated with 1 mM L-cysteine and 0.5 μM EDTA in Earle's Balanced Salt Solution (EBSS) (Thermo Fisher), and DNase I (Worthington) added. hMLOs were finely chopped with a scalpel and then resuspended in papain enzyme mix. The slurry was incubated at 37°C, 5% CO2 for 45 min on a rotator, and then triturated. Cells were spun down at 300xg for 5 min and washed twice in EBSS containing ovalbumin (Worthington) and BSA.

treatment_protocol: Cell lines were generated via CRISPR/Cas9 genome editing using similar methods as previously reported7, using gRNAs (5’-GATTTGACTGACCGCCAGCGTGG-3’ and 5’-GTTCGCTCTAAACAAAACAGTGG-3’) cloned into the lentiCRISPRv2 plasmid (Addgene plasmid #52961) to mediate knockout of the PARK7 gene.

tag: tag


title: MLO_WT_organoid_2_replicate_2

description: GIS-Human-140-v1.0; Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015). RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science (New York, N.Y.), 348(6233), aaa6090. https://doi.org/10.1126/science.aaa6090

label_protocol: RNA spots were decoded from the codebook using logic outlined in section “design and construction of the MERFISH encoding probes”.

tag: organoid id

tag: genotype

value: WT

tag: age


title: COJO-PBMC-TIL-1-D13

description: Library name: S11732Nr47


title: MLO_WT_organoid_2_replicate_1


title: COJO-PBMC-TIL-1-D3

description: Library name: S11732Nr46


title: MLO_WT_organoid_2_replicate_4


title: COJO-TIL-1

description: Library name: S11732Nr44


title: Atsdr4l-5 dig2, seed coat, rep 3

city: Vancouver

first: Liang

last: Song

state: British Columbia

address: 2231-6270 University Boulevard

department: Botany

country: Canada

institute: University of British Columbia

description:
Library name: S008_12_CKDL240034832-1A_22HNCMLT4_L4
S008_12_CKDL240034832-1A_22HNCMLT4_L4

data_processing:
Fastq files were generated and demultiplexed using bcl2fastq version 2.19 with mismatch set to 0.
Raw sequencing reads were preprocessed with fastp 0.12.4 with the default parameters for adaptor trimming.
Filtered reads were aligned to the Arabidopsis TAIR10 reference genome with Araport11 annotation using STAR 2.7.9a and the arguments “--runMode alignReads --outFilterMultimapNmax 10 --outFilterMismatchNoverLmax 0.05 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx”.
Read count data were extracted from the fourth column of the “ReadsPerGene.out.tab” output file to combine all samples into one read count matrix.
Assembly: TAIR10
Supplementary files format and content: tab-delimited (.tab) file with the raw read counts for each sample
Supplementary files format and content: tab-separated values (.tsv) file with the raw read counts from all samples, with each column corresponding to one sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seed coat

growth_protocol: Atsdr4l-5 dig2 and Col-0 plants were grown under the “long-day” condition (16 h light at 23°C / 8 h dark at 18°C). Seeds were collected at maturity when siliques turned yellow-to-brown (approximately 18 days after pollination).

extract_protocol:
Seeds were gently pressed between two microscope glass slides to break the seed coats. Endosperm (with seed coat) and intact embryos were manually separated using syringe needles and fine forceps and preserved in RNAlater buffer (AM7020, Thermo Fisher Scientific, Waltham, MA, USA) in a microcentrifuge tube until all samples have been collected. Total RNA was isolated using Spectrum™ Plant Total RNA Kit (STRN50, MilliporeSigma, Burlington, MA, USA), followed by the removal of genomic DNA by DNase I treatment (AM1907, TURBO DNA-free™ Kit, Thermo Fisher Scientific, Waltham, MA, USA).
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (E7760S, NEB, Ipswich, MA, USA) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and Unique Dual Index UMI Adaptors RNA Set 1 (E7416S, NEB, Ipswich, MA, USA) were used for library preparation following the manufacturer's instructions.

treatment_protocol: Seeds were briefly stored for 2 days at room temperature, and then shortly imbibed in water for 1 to 2 hours for softening the seed coat before isolating embryos and the endosperm (within seed coat).

value: seed coat

value: Atsdr4l-5 dig2

value: mature seeds


title: COJO-PBMC-Pre-TIL-1

description: Library name: S11732Nr43


title: COJO-PBMC-TIL-3-Y3

description: Library name: S11732Nr25


title: Atsdr4l-5 dig2, embryo, rep 2

description:
Library name: S008_09_CKDL240034832-1A_22HNCMLT4_L4
S008_09_CKDL240034832-1A_22HNCMLT4_L4

source_name: embryo

value: embryo


title: COJO-PBMC-TIL-3-Y5

description: Library name: S11732Nr26


title: Atsdr4l-5 dig2, seed coat, rep 2

description:
Library name: S008_10_CKDL240034832-1A_22HNCMLT4_L4
S008_10_CKDL240034832-1A_22HNCMLT4_L4


title: MLO_WT_organoid_6_replicate_1


title: Atsdr4l-5 dig2, seed coat, rep 1

description:
Library name: S008_08_CKDL240034832-1A_22HNCMLT4_L4
S008_08_CKDL240034832-1A_22HNCMLT4_L4


title: COJO-PBMC-TIL-3-Y2

description: Library name: S11732Nr24


title: Atsdr4l-5 dig2, embryo, rep 1

description:
Library name: S008_07_CKDL240034832-1A_22HNCMLT4_L4
S008_07_CKDL240034832-1A_22HNCMLT4_L4


title: COJO-PBMC-TIL-3-M13

description: Library name: S11732Nr23


title: COJO-PBMC-D51-PD1-Dose4

description: Library name: S11732Nr21


title: Col-0, seed coat, rep 2

description:
Library name: S008_04_CKDL240034832-1A_22HNCMLT4_L4
S008_04_CKDL240034832-1A_22HNCMLT4_L4


title: COJO-PBMC-D7-PD1-Dose2

description: Library name: S11732Nr20


title: Col-0, embryo, rep 2

description:
Library name: S008_03_CKDL240034832-1A_22HNCMLT4_L4
S008_03_CKDL240034832-1A_22HNCMLT4_L4


title: Col-0, seed coat, rep 3

description:
Library name: S008_06_CKDL240034832-1A_22HNCMLT4_L4
S008_06_CKDL240034832-1A_22HNCMLT4_L4


title: COJO-PBMC-D7-PD1-Dose1

description: Library name: S11732Nr19


title: MLO_WT_organoid_2_replicate_3


title: Col-0, embryo, rep 3

description:
Library name: S008_05_CKDL240034832-1A_22HNCMLT4_L4
S008_05_CKDL240034832-1A_22HNCMLT4_L4


title: Col-0, seed coat, rep 1

description:
Library name: S008_02_CKDL240034832-1A_22HNCMLT4_L4
S008_02_CKDL240034832-1A_22HNCMLT4_L4


title: COJO-PBMC-TIL-3-D3

description: Library name: S11732Nr16


title: COJO-PBMC-TIL-3-M10

description: Library name: S11732Nr22


title: COJO-PBMC-TIL-1-D1

description: Library name: S11732Nr45


title: COJO-PBMC-TIL-3-D7

description: Library name: S11732Nr17


title: COJO-PBMC-TIL-3-D1

description: Library name: S11732Nr15


title: Col-0, embryo, rep 1

description:
Library name: S008_01_CKDL240034832-1A_22HNCMLT4_L4
S008_01_CKDL240034832-1A_22HNCMLT4_L4


title: nanobody

first: J.

middle: Ian

last: Hertzler

address: 3745 W Stevens Wy NE

department: Biology

description: Library name: Sample 3

library_source: transcriptomic single cell

data_processing:
Demultiplexing done by sequencing facility (UCSF Cat Core). Received fastq files.
Each genotype was run through CellRanger Count function individually with a custom reference genome. The base Drosophila Melanogaster genome was downloaded from Ensembl (release 112), and sequences for GFP and mCherry were added to the .gtf and .fa files.
Quality control was done on each genotype individually, then all three were integrated into a single dataset in Seurat.
Assembly: Ensembl Drosophila Melanogaster, release 112
Supplementary files format and content: tsv and mtx files

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Larvae grown at 25C on standard molasses/corn meal media plates.

extract_protocol: 10x manual followed to the T: https://cdn.10xgenomics.com/image/upload/v1710230393/support-documents/CG000731_ChromiumGEM-X_SingleCell3_ReagentKits_v4_UserGuide_RevA.pdf

treatment_protocol: No treatment apart from genotype.

value: larval brain

value: 72-96hr AEL

value: neuroblasts and neurons

value: Sqh::GFP ; worGal4, UAS-mCherry::Jupiter, UAS-ALDInscuteable RockKinase domain-VhhGFP4-HA on 3

tag: batch


title: COJO-PBMC-Pre-PD1

description: Library name: S11732Nr18


title: control

description: Library name: Sample 1

value: Sqh::GFP on X ; worGal4, UAS-mCherry::Jupiter on 3


title: MON-FIA-2_S71

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

description:
Library name: MON-FIA-2_S71
normcounts_monkey.csv
qc_hash_monkey.csv

data_processing:
The gene count matrices were generated from paired-end reads with 2 lanes per sample with ~150 base pairs (bp).
The reads from the 2 lanes for each sample were combined to generate a single fastq file.
Reads were quality trimmed using fastp (version 0.23.2) with the following steps: (1) automatic detection of adapter sequences for paired-end reads, (2) trimming of homopolymer stretches, and (3) removal of bases with Phred quality scores below 20 (Chen et al., 2018).
Reads were aligned to the species-specific genome assembly using STAR version 2.7.10b (Dobin et al. 2013). Aligned reads were sorted with SAMtools version 1.14 (Danecek et al. 2021), and gene-level counts were generated using HTSeq version 2.0.1 (Anders et al. 2014).
Samples with fewer than 1 million total counts or with uniquely mapped reads below 50% were excluded from further analysis. For transcript-level quality control, transcripts that were not expressed across the entire sample set for each species were removed. The Bioconductor package DESeq2 (Love et al., 2014) was used to perform within-species normalization and differential expression analysis across all experimental conditions.
Assembly: Reads from dog, monkey, human, and rat were mapped to the ROS_Cfam_1.0, Macaca_fascicularis_6.0, GRCh38, and mRatBN7 genome assemblies, respectively, using STAR. Gene annotations from Ensembl GTF files corresponding to each assembly were used for quantification.
Supplementary files format and content: normcounts_* files contain normalized count data using DESeq2 R package (Love et al., 2014) for each species
Supplementary files format and content: qc_hash* files contain meta data of the qc-passed samples for each species

organism: Macaca fascicularis

source_name: hepatocytes

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and the Direct-zol RNA Miniprep (Zymo, USA) following the manufacturer’s protocol with slight modifications detailed here. MPS Scaffolds from each experiment were preserved in RNAlater at -80°C until RNA extraction. On the day of extraction, samples were thawed at room temperature, and each scaffold was cut into two pieces before transferring to a 1.5 mL microcentrifuge tube. Next, 700 µL of TRIzol reagent was added to the samples, which were then incubated at room temperature for 20 minutes. During incubation, the samples were vortexed for 30 seconds every 5 minutes to ensure complete lysis. The scaffolds were removed from the microcentrifuge and the RNA was precipitated using equal volume of 100% molecular grade ethanol, then transferred to a Zymo-Spin™ IICR column. The remainder of the extraction was performed according to the standard protocol. RNA was eluted in 60 uL of DNAase/RNAse free water.
mRNA was isolated from 150ng total RNA using a Nextflex Poly-A Selection kit. Unique dual indexed cDNA libraries were prepared on a Sciclone NGSx liquid handler, using a Nextflex Rapid Directional RNA 2.0 kit miniaturized to 2/5 reaction volume. Optimal PCR cycle count was empirically determined to be 17 by cycling a pool of samples to the plateau phase on a real-time PCR machine. The concentration of libraries was determined using a Molecular Devices (San Jose, CA) Spectramax M2 fluorescent plate reader and Thermo Fisher Scientific (Waltham, MA) Picogreen Assay. Libraries were then pooled by equal mass using a Janus Mini liquid handler. The libraries were pooled by equal mass. The pool was sequenced on a Illumina (San Diego, CA) NovaSeq X+ 1.5B flowcell using the 2x150 bp recipe.

value: hepatocytes

value: fialuridine


title: Atsdr4l-5 dig2, embryo, rep 3

description:
Library name: S008_11_CKDL240034832-1A_22HNCMLT4_L4
S008_11_CKDL240034832-1A_22HNCMLT4_L4


title: MDA-MB-231 cells, siNC_3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

country: China

institute: Nissi Biotech

description: Library name: siNC_3

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After that, clean reads were aligned to the human human_gencode_v38 genome by HISAT2 allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2 was utilized to screen out the differentially expressed genes (DEGs). The FDR < 0.05 and fold change ≥ 2 or ≤ 1/2 were set as the cut-off criteria for identifying DEGs.
Assembly: hg38
Supplementary files format and content: Expression profile with FPKM values for all detected genes.
Supplementary files format and content: Expression profile with raw reads count for all detected genes.

source_name: cell line

growth_protocol: The MDA-MB-231 cells line (CL-0150B, Procell Life Science & Technology Co., Ltd., China) were cultured at 37℃ with 5% CO2 in DMEM (PM150210, Procell Life Science & Technology Co., Ltd., China) with 10% fetal bovine serum (FBS) (10091148, Gibco, China), 100 µg/mL streptomycin, 100 U/mL penicillin (SV30010, Hyclone, USA).

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional RNA-seq library preparation by VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (N605) for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads (Vazyme, N401). Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina (N323), the ligated products were amplified, purified, quantified, and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.

treatment_protocol: The siRNA duplexes were constructed from Gemma (Suzhou, China). The non-targeting control siRNA (siNC) sequences were 5'-UUCUCCGAACGUGUCACGUTT-3’(sense). The targeting SF3B6 (siSF3B6) sequences were 5'- GGAGGAACAGUUGAAGCUUTT -3’ (sense). The siRNA transfection was performed using Lipofectamine™ RNAi MAX Transfectn Reagent (13778030, Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.

value: cell line

value: MDA-MB-236 cells

value: breast cancer

value: negative control


title: MON-FIA-3_S72

description:
Library name: MON-FIA-3_S72
normcounts_monkey.csv
qc_hash_monkey.csv


title: COJO-Tumor-Pre-TIL-1

description: Library name: S11732Nr1

source_name: tumor

value: tumor

value: autologous tumor line

value: prostate cancer


title: MON-FIA-1_S70

description:
Library name: MON-FIA-1_S70
normcounts_monkey.csv
qc_hash_monkey.csv


title: COJO-Tumor-Pre-TIL-3

description: Library name: S11732Nr13


title: MON-D8-3_S21

description:
Library name: MON-D8-3_S21
normcounts_monkey.csv
qc_hash_monkey.csv


title: mud

description: Library name: Sample 2

value: Sqh::GFP, mud4 on X ; worGal4, UAS-mCherry::Jupiter on 3


title: MDA-MB-231 cells, siNC_2

description: Library name: siNC_2

value: MDA-MB-235 cells


title: MDA-MB-231 cells, siNC_1

description: Library name: siNC_1

value: MDA-MB-234 cells


title: MON-D8-2_S20

description:
Library name: MON-D8-2_S20
normcounts_monkey.csv
qc_hash_monkey.csv


title: MDA-MB-231 cells, siSF3B6_1

description: Library name: siSF3B6_1

value: MDA-MB-231 cells

value: SF3B6 knockdown


title: MDA-MB-231 cells, siSF3B6_2

description: Library name: siSF3B6_2

value: MDA-MB-232 cells


title: MON-D4-3_S18

description:
Library name: MON-D4-3_S18
normcounts_monkey.csv
qc_hash_monkey.csv


title: MON-D4-1_S16

description:
Library name: MON-D4-1_S16
normcounts_monkey.csv
qc_hash_monkey.csv


title: MDA-MB-231 cells, siSF3B6_3

description: Library name: siSF3B6_3

value: MDA-MB-233 cells


title: MON-D4-2_S17

description:
Library name: MON-D4-2_S17
normcounts_monkey.csv
qc_hash_monkey.csv


title: MDA-MB-231 cells, Input 1

description: Library name: Input_1

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
After reads were aligned onto the genome with HISAT2, the unique comparison on the genome was finally obtained, and the comparison result of PCR duplicate was removed.
Piranha and ABLIRC, were used to perform peak calling. Piranha has been described elsewhere. “ABLIRC” strategy was used to identify the binding regions of RNA binding protein on genome-wide scale.
The target genes of IP were finally determined by the peaks and the binding motifs of IP protein were called by HOMER software.
Assembly: hg38
Supplementary files format and content: Expression profile with FPKM values for all detected genes.
Supplementary files format and content: Expression profile with raw reads count for all detected genes.

extract_protocol:
For immunoprecipitation, the supernatant was incubated overnight at 4°C with 5 μg SF3B6 antibody (thermo: PA5-57077) and control IgG-antibody (AC005). The immunuprecipitates were further incubated with protein A/G Dynabeads (Thermo Scientific) for 2h at 4°C. After applying to magnet and removing the supernatants, the beads were sequentially washed with lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) and high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5 deoxycholate), respectively. Resuspend the beads in of Elution buffer (50 mM Tris 8.0, 10 mM EDTA and 1% SDS).
The RNA was purified with Phenol: chloroform: isopentyl alcohol (25:24:1 pH<5) reagent (Solarbio). The cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8544) according the manufacturer’s procedure.

treatment_protocol: MDA-MB-231 cells were irradiated once for 400 mJ/cm2, and lysed in ice-cold wash buffer. Cells lysis was performed in cold Wash buffer (1×PBS, 0.5% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 400 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Bimake) and incubate on ice for 30 min. Add RQ I (Promega, 1 U/μl) to a final concentration of 0.1 U/μl and incubate in a heat block for 30 min at 37°C. The mixture was then vibrated vigorously and centrifuged at 13,000 xg at 4℃ for 15 min to remove cell debris. Then RNA digestion by MNase was performed. EDTA was added to stop digestion.

value: RNA Input control


title: MDA-MB-231 cells, Input 2

description: Library name: Input_2


title: MON-D14-2_S23

description:
Library name: MON-D14-2_S23
normcounts_monkey.csv
qc_hash_monkey.csv

value: hepatocytes


title: MON-D14-3_S24

description:
Library name: MON-D14-3_S24
normcounts_monkey.csv
qc_hash_monkey.csv


title: Drug 1

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

institute: Shanghai Jiao Tong University

description: Library name: Sample 2

library_source: genomic

data_processing:
Cut&tag technology will insert the linker sequence into the DNA near the antibody linked pa-tn5.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: liver cancer

growth_protocol: DMEM, 15% fetal bovine serum, 1× penicllin/streptomycin.Cells were cultured at 37℃ at 5%CO2.

extract_protocol:
The CUT&Tag assay was performed in PLC8024 cells using the NovoNGS® CUT&Tag® 4.0 High-Sensitivity Kit (designed for Illumina®) (Novoprotein, N259-YH01, Shanghai, China), following the manufacturer’s instructions.
10ng of DNA was used as starting material for ip samples. Libraries were amplidied using 13 cyclies on the thermocycler. Post amplification libraries were size selected at 250-450bp in length.

value: liver cancer

value: tumor cell line

value: drug


title: MDA-MB-231 cells, SF3B6 IP 2

description: Library name: SF3B6_IP_2

value: cell line

value: SF3B6 Immunoprecipitation


title: MON-D14-1_S22

description:
Library name: MON-D14-1_S22
normcounts_monkey.csv
qc_hash_monkey.csv


title: MON-D0-3_S15

description:
Library name: MON-D0-3_S15
normcounts_monkey.csv
qc_hash_monkey.csv


title: Control 1

description: Library name: Sample 1

value: control


title: MON-D0-1_S13

description:
Library name: MON-D0-1_S13
normcounts_monkey.csv
qc_hash_monkey.csv


title: CD8+ effector T cells, scrambled control, experiment 1, donor 122

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

country: Germany

institute: Helmholtz-Centre for Infection Research

description: Library name: D122-scr-1

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 using the NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run) with an average of 5 x 107 reads per sample. For processing and analysis, raw reads (.fastq files) were imported into the CLC Genomics Workbench 23.0.4 (Qiagen) as paired reads for further analysis. The quality of the raw reads was checked and adapters were excluded with a quality score limit of 0.05 and maximum number of ambiguities of 2. The trimmed sequences were then mapped to the human genome hg38 reference genome using standard alignment settings: match score 1, mismatch cost 2, gap cost 3, length fraction 0.5 and similarity fraction 0.8. Differential expression analyses were performed using gene expression (GE) tracks generated by the "RNA Seq Analysis" tool, and data were normalised using the Trimmed Mean of M method.
Assembly: GRCh38
Supplementary files format and content: DEG table obtained from the ZEB2 knockout vs.scrambled control comparison in CSV format containing the gene name, log2 fold change, P-value, FDR p-value, ENSEMBL gene ID.

source_name: peripheral blood

extract_protocol:
Total RNA was prepared from the cultured cells by using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol. The RNA quality was analyzed by using an Agilent 2100 Bioanalyzer (all RNA Integrity Number (RIN) >7). The RNAseq library was generated from 500 ng total RNA of each sample.
The RNAseq library was generated by using the Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by the NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs).

treatment_protocol: The CD8+ T cells were enriched from peripheral blood of healthy, human donors by using anti-CD8-Microbeads and the autoMACS Pro (Miltenyi Biotec) magnetic separation system. The enriched cells were stained with antibodies and sorted into CD8+ effector cells(CD3+CD8+CD45RA−/+CCR7−) by using a BD Biosciences Aria II flow cytometer. After 5 days of pre-stimulation of CD8+ effector T cells with plate-bound anti-CD3 (1 µg/ml) and anti-CD28 (0.5 µg/ml) antibodies, CRISR/Cas9 ribonucleoprotein complexes were transferred into the cells by nucleofection( Lonza). Transfected cells were cultured overnight in TexMACS medium (Miltenyi Biotec) supplemented with 100 IU/ml rhIL 2 and then stimulated with plate-bound anti CD3 and anti CD28 antibodies (both 0.5 μg/ml) for a further 2 days in TexMACS medium supplemented with 100 IU/ml rhIL 2.

value: peripheral blood

value: CD8+ effector T cells

tag: marker

value: Electroporation of CRISPR/Cas9 ribonucleoprotein complex (containing non-targeting Alt-R® CRISPR Cas9 Negative Control crRNA #1 (IDT)), 2 days stimulation with plate-bound anti-CD3 and anti-CD28 antibodies (both 0.5µg/ml).


title: MON-CPZ-1_S64

description:
Library name: MON-CPZ-1_S64
normcounts_monkey.csv
qc_hash_monkey.csv

value: chlorpromazine


title: CD8+ effector T cells, scrambled control, experiment 2, donor 122

description: Library name: D122-scr-2


title: CD8+ effector T cells, ZEB2 knockout, experiment 2, donor 122

description: Library name: D122-ko-2

value: Electroporation of CRISPR/Cas9 ribonucleoprotein complex (containing ZEB2 specific Alt-R® CRISPR Cas9 cRNAs (IDT), 2 days stimulation with plate-bound anti-CD3 and anti-CD28 antibodies (both 0.5µg/ml).


title: MON-CPZ-2_S65

description:
Library name: MON-CPZ-2_S65
normcounts_monkey.csv
qc_hash_monkey.csv


title: CD8+ effector T cells, ZEB2 knockout, experiment 2, donor 121

description: Library name: D121-ko-2


title: CD8+ effector T cells, ZEB2 knockout, experiment 1, donor 121

description: Library name: D121-ko-1


title: MON-CON-3_S63

description:
Library name: MON-CON-3_S63
normcounts_monkey.csv
qc_hash_monkey.csv

value: DMSO control


title: MON-CON-2_S62

description:
Library name: MON-CON-2_S62
normcounts_monkey.csv
qc_hash_monkey.csv


title: MON-D8-1_S19

description:
Library name: MON-D8-1_S19
normcounts_monkey.csv
qc_hash_monkey.csv


title: CD8+ effector T cells, scrambled control, experiment 1, donor 121

description: Library name: D121-scr-1


title: MON-CON-1_S61

description:
Library name: MON-CON-1_S61
normcounts_monkey.csv
qc_hash_monkey.csv


title: CD8+ effector T cells, scrambled control, experiment 2, donor 121

description: Library name: D121-scr-2


title: CD8+ effector T cells, ZEB2 knockout, experiment 1, donor 120

description: Library name: D120-ko-1


title: MDA-MB-231 cells, SF3B6 IP 1

description: Library name: SF3B6_IP_1

value: MDA-MB-231 cells


title: MON-BOS-2_S68

description:
Library name: MON-BOS-2_S68
normcounts_monkey.csv
qc_hash_monkey.csv

value: bosentan


title: CD8+ effector T cells, ZEB2 knockout, experiment 2, donor 120

description: Library name: D120-ko-2


title: CD8+ effector T cells, scrambled control, experiment 2, donor 120

description: Library name: D120-scr-2


title: CD8+ effector T cells, scrambled control, experiment 1, donor 120

description: Library name: D120-scr-1

value: Electroporation of CRISPR/Cas9 ribonucleoprotein complex (containing non-targeting Alt-R® CRISPR Cas9 Negative Control crRNA #1 (Integrated DNA Technologies (IDT))), 2 days stimulation with plate-bound anti-CD3 and anti-CD28 antibodies (both 0.5µg/ml).


title: MON-BOS-1_S67

description:
Library name: MON-BOS-1_S67
normcounts_monkey.csv
qc_hash_monkey.csv


title: FolWT, axenic RNA-seq, biol rep 4

city: Jena

first: Tongta

last: Sae-Ong

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)

description: Library name: F4_Fol4287

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using FastP v.0.23.4 (parameters --qualified_quality_phred=20, --detect_adapter_for_pe)
For RNA-seq: Trimmed sequence reads were mapped to Fusarium oxysporum f. sp. lycopersici (Fol) and Tomato (SL3.0) genome using bbsplit (from Bbmap v.39.13) to get Fusarium- and tomato-specific reads
For RNA-seq: Trimmed sequence reads were mapped to Fusarium oxysporum f. sp. lycopersici (Fol) and tomato genomes using Hisat2 v2.2.1
For RNA-seq: Reads were counted per feature using Rsubread’s featureCounts v.2.0.8
For ChIP-seq: Trimmed sequence reads were mapped to Fusarium graminearum genome using bowtie2 v.2.5.4
For ChIP-seq: PCR duplicates were removed form BAM files using Picard v3.4.0
For ChIP-seq: Reads were normalized using bamCoverage deeptools v.3.5.6 (parameters --normalizeUsing RPGC --effectiveGenomeSize 36458046 --binSize 500 --extendReads 150 --smoothLength 150 –centerReads)
Assembly: UvA_Fol4287 (GCA_001703175.2), Fg (GCA_000240135.3), Tomato (SL3.0)
Supplementary files format and content: TSV files: Tab-delimated txt files including matrix of raw read count values for every sample (*_RawCounts.xls)
Supplementary files format and content: BW files: Bam coverage tracks in bigwg format

organism: Fusarium oxysporum f. sp. lycopersici

extract_protocol:
RNA-seq: isolation of total RNA using Trizol reagent according to the manufacturer's instructions. ChIP-seq: cross-linking, antibody hybridization, de-crosslinking and purification of gDNA as previously described (Janevska et al., 2018, Genetics 208: 153-171)
PolyA enrichment for RNA-seq (library preparation and sequencing by Novogene), ChIP-seq library preparation and sequencing also by Novogene

value: Vegetative mycelium

value: FolWT


title: hNPC6, OE, Rep2

city: Houston

first: Marco

last: Gallo

state: Texas

address: 1102 Bates Avenue

institute: Baylor College of Medicine

description: Library name: Sample 8

data_processing:
nf-core/rnaseq revision 3.14.0 aligner star_rsem
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz Homo_sapiens.GRCh38.111.gtf.gz
Supplementary files format and content: Plain text file includes raw count for each sample

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
Libraries were constructed at the Center for Health Genomics and Informatics at the University of Calgary Cumming School of Medicine using the NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) with ribosomal RNA depletion.

value: OE


title: MON-D0-2_S14

description:
Library name: MON-D0-2_S14
normcounts_monkey.csv
qc_hash_monkey.csv

value: hepatocytes


title: FolWT, axenic RNA-seq, biol rep 2

description: Library name: F2_Fol4287


title: hNPC6, OE, Rep1

description: Library name: Sample 7


title: FolWT, axenic RNA-seq, biol rep 1

description: Library name: F1_Fol4287


title: MON-CPZ-3_S66

description:
Library name: MON-CPZ-3_S66
normcounts_monkey.csv
qc_hash_monkey.csv


title: CD8+ effector T cells, ZEB2 knockout, experiment 1, donor 122

description: Library name: D122-ko-1


title: hNPC5, OE, Rep2

description: Library name: Sample 4


title: hNPC6, Control, Rep1

description: Library name: Sample 5

value: Control


title: Δkmt6a, in planta RNA-seq, biol rep 1

description: Library name: kmt_A

value: Root infection


title: Δkmt6a, in planta RNA-seq, biol rep 3

description: Library name: kmt_C


title: Δkmt6a, in planta RNA-seq, biol rep 2

description: Library name: kmt_B


title: hNPC5, OE, Rep1

description: Library name: Sample 3


title: FolWT, in planta RNA-seq, biol rep 3

description: Library name: wt_C


title: MON-BOS-3_S69

description:
Library name: MON-BOS-3_S69
normcounts_monkey.csv
qc_hash_monkey.csv


title: hNPC5, Control, Rep2

description: Library name: Sample 2


title: FolWT, in planta RNA-seq, biol rep 2

description: Library name: wt_B


title: hNPC5, Control, Rep1

description: Library name: Sample 1


title: FolWT, in planta RNA-seq, biol rep 1

description: Library name: wt_A


title: Blood, Control, Black, Patient 117

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

description:
Library name: Patient_117
TWIST

data_processing:
Mapping to hg38 was done with dnmtoools.
Further analysis including processing into relative abundance and differential abundance analysis was done with methylKit
Assembly: hg38
Supplementary files format and content: File includes C and T counts, and coverage for each CpG. Tab-seperated Matrix

extract_protocol:
DNA was extracted using the Autogen Fresh/Universal Flexigene Kit and FlexStar+ instrument
A Quality Control analysis was performed on the DNA samples using a DNA Picogreen assay to determine quantity.  The samples were normalized, and libraries were prepared using the NEBNext® Enzymatic Methyl-seq kit (P/N: E7120L) following a modified version of the manufacturers protocol.  The libraries were pooled (95-plex) and captured using the Human Methylome panel from Twist Biosciences (P/N: 105521).  The pool quality was assessed post-hybridization using the Agilent Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument.

value: Blood

tag: disease state

tag: self-reported race

value: Black

tag: self-reported sex

value: Female


title: Blood, Control, Black, Patient 116

description:
Library name: Patient_116
TWIST


title: scRNA-seq of mus musculus: adult male thymus BM-MSC1

city: Guangzhou

first: Haotong

last: Yi

state: Guangdong Province

address: 600 TIANHE ROAD

department: Department of Neurology

institute: the Third Affiliated Hospital of Sun Yat-sen University

description: Library name: scRNA_BM-MSC1_R1

data_processing:
For BulkRNA-seq: Rawdata(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.
For scRNA-se:Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Assembly: mm39
Supplementary files format and content: For BulkRNA-seq:csv files include FPKM values for each Sample; For scRNA-seq:h5 files for each Sample

organism: Mus musculus

source_name: thymus

extract_protocol:
BulkRNA-seq &scRNA-seq
For BulkRNA-seq:RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries. For scRNA-seq:The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10XGenomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq ,depends on project) according to the manufacturer’s instructions (Illumina).

value: thymus

value: adult

tag: Sex

value: male

value: BM-MSC


title: FolWT, axenic RNA-seq, biol rep 3

description: Library name: F3_Fol4287


title: Blood, Control, Black, Patient 115

description:
Library name: Patient_115
TWIST


title: Blood, Control, Black, Patient 114

description:
Library name: Patient_114
TWIST

value: Male


title: scRNA-seq of mus musculus: adult male thymus Veh1

description: Library name: scRNA_Veh1_R1

value: Veh


title: BulkRNA-seq of mus musculus: adult male thymus Migrasome4

description: Library name: Bulk_Migrasome4_1

value: Migrasome


title: Blood, PAD, Black, Patient 113

description:
Library name: Patient_113
TWIST

value: PAD


title: hNPC6, Control, Rep2

description: Library name: Sample 6


title: Blood, PAD, Black, Patient 112

description:
Library name: Patient_112
TWIST


title: Blood, PAD, Black, Patient 111

description:
Library name: Patient_111
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus Migrasome1

description: Library name: Bulk_Migrasome1_1


title: Blood, PAD, Black, Patient 110

description:
Library name: Patient_110
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus BM-MSC4

description: Library name: Bulk_BM-MSC4_1


title: Blood, PAD, Black, Patient 109

description:
Library name: Patient_109
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus BM-MSC3

description: Library name: Bulk_BM-MSC3_1


title: Blood, PAD, Black, Patient 108

description:
Library name: Patient_108
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus BM-MSC2

description: Library name: Bulk_BM-MSC2_1


title: BulkRNA-seq of mus musculus: adult male thymus BM-MSC1

description: Library name: Bulk_BM-MSC1_1


title: Blood, PAD, Black, Patient 106

description:
Library name: Patient_106
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus Veh4

description: Library name: Bulk_Veh4_1


title: Blood, PAD, Black, Patient 105

description:
Library name: Patient_105
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus Veh3

description: Library name: Bulk_Veh3_1


title: scRNA-seq of mus musculus: adult male thymus Migrasome1

description: Library name: scRNA_Migrasome1_R1


title: Blood, PAD, Black, Patient 104

description:
Library name: Patient_104
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus Veh2

description: Library name: Bulk_Veh2_1


title: Blood, PAD, Black, Patient 103

description:
Library name: Patient_103
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus Veh1

description: Library name: Bulk_Veh1_1


title: Blood, Control, White, Patient 102

description:
Library name: Patient_102
TWIST

value: White


title: Blood, Control, White, Patient 101

description:
Library name: Patient_101
TWIST


title: BulkRNA-seq of mus musculus: adult male thymus Migrasome3

description: Library name: Bulk_Migrasome3_1


title: BulkRNA-seq of mus musculus: adult male thymus Migrasome2

description: Library name: Bulk_Migrasome2_1


title: 688M PDA cells, WGS, shKdm8_2, replicate 1

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

institute: Rutgers Cancer Institute of New Jersey

description: Library name: Sample 3

data_processing:
Briefly, fastq files from the WGS studies were mapped to an mm39 reference prior to alignments using bowtie2 (v2.4.1). To compute bin boundaries, mm39 fasta files for individual chromosomes were downloaded from UCSC (hgdownload.cse.ucsc.edu/goldenPath/mm39/chromosomes) and used to generate reads from the reference genome. The reads were mapped back to the mm39 reference using bowtie2 and the result was used to generate genomic positions that defined 50,000 bins with equal numbers of mappable positions. Counts of reads within the bins were quantified for each sample with the GC content accounted for. Genomic distribution of WGS signals and the copy number estimation were derived and plotted using custom R codes.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files

source_name: Pancreatic

growth_protocol: PDA 688M cells expressing the control or Kdm8-targeting shRNAs (shKdm8_1 and shKdm8_2) were maintained in DMEM media with 10% FBS and antibiotics in humidified 5% CO2 at 37C

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit (69504, Qiagen) per the manufacturer's protocol.
The libraries were prepared using the Rapid Plus DNA Lib Prep Kit (ABclonal) prior to sequencing on a NovaSeq X Plus sequencer (Novogene).

treatment_protocol: PDA 688M cells were either cultured in normoxia (atmospheric O2) prior to gDNA extraction using the Qiagen DNeasy Blood and Tissue Kit (69504, Qiagen).

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells

value: normoxia


title: 688M PDA cells, WGS, shKdm8_1, replicate 1

description: Library name: Sample 2


title: Blood, Control, White, Patient 100

description:
Library name: Patient_100
TWIST

value: Control


title: 688M PDA cells, WGS, shGFP, replicate 1

description: Library name: Sample 1


title: B16F10 cells,  ΔUNG, ATRi, 48h, bio replicate 2

city: Pittsburgh

first: Christopher

middle: J

last: Bakkenist

state: PA

address: 5051 Centre Avenue

department: Radiation oncology

institute: university of pittsburgh

description:
Library name: CRRA220040017-1a
Column name in all genes fpkm value.xlsx: CB_12

data_processing:
All the analysis, including raw read collections, trimming step, allignement to reference and final gene expression in FPKM is proceessed by Novogen.
Sequence reads were trimmed for adaptor sequence, uncertain nucleotide constitute (N > 10%) and low-quality sequence using Novogen standard genomic platform.
Assembly: High quality sequence reads were alligned to reference genome using HISAT2.
Supplementary files format and content: xlsx files include FPKM values for each Sample

growth_protocol: B16F10 cells (control and knockout) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penstrip in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep kit (Zymo research). 2ug total RNA was sent to Novogene Corporation Inc. (Sacramento, CA) for the RNA sequencing and analysis step.
RNA libraries for RNA-seq were prepared by Novogen using standard protocol.

treatment_protocol: Cells were treated with DMSO or 5uM ATRi (AZD6738) for 48h.

value: Melanoma

value: UNG knockout

value: ATRi (AZD6738)

tag: time


title: Blood, Control, White, Patient 98

description:
Library name: Patient_98
TWIST

value: Blood


title: Blood, PAD, Black, Patient 107

description:
Library name: Patient_107
TWIST

value: Black


title: Blood, Control, White, Patient 97

description:
Library name: Patient_97
TWIST

value: Female


title: B16F10 cells,  ΔUNG_2, ATRi, 48h, bio replicate 1

description:
Library name: CRRA220040014-1a
Column name in all genes fpkm value.xlsx: CB_9


title: B16F10 cells,  ΔUNG, ATRi, 48h, bio replicate 1

description:
Library name: CRRA220040016-1a
Column name in all genes fpkm value.xlsx: CB_11


title: Blood, Control, White, Patient 96

description:
Library name: Patient_96
TWIST


title: B16F10 cells, cas9 control, ATRi, 48h, bio replicate 1

description:
Library name: CRRA220040012-1a
Column name in all genes fpkm value.xlsx: CB_7

value: WT


title: B16F10 cells, cas9 control, ATRi, 48h,bio replicate 2

description:
Library name: CRRA220040013-1a
Column name in all genes fpkm value.xlsx: CB_8


title: B16F10 cells,  ΔUNG, DMSO, 48h, bio replicate 2

description:
Library name: CRRA220040011-1a
Column name in all genes fpkm value.xlsx: CB_6

value: DMSO


title: Blood, Control, White, Patient 94

description:
Library name: Patient_94
TWIST

value: Male


title: B16F10 cells,  ΔUNG_2, DMSO, 48h, bio replicate 1

description:
Library name: CRRA220040008-1a
Column name in all genes fpkm value.xlsx: CB_3


title: Blood, Control, White, Patient 95

description:
Library name: Patient_95
TWIST


title: B16F10 cells, cas9 control, DMSO, 48h, bio replicate 2

description:
Library name: CRRA220040007-1a
Column name in all genes fpkm value.xlsx: CB_2


title: Blood, Control, White, Patient 90

description:
Library name: Patient_90
TWIST


title: B16F10 cells,  ΔUNG, DMSO, 48h, bio replicate 1

description:
Library name: CRRA220040010-1a
Column name in all genes fpkm value.xlsx: CB_5


title: Blood, Control, White, Patient 92

description:
Library name: Patient_92
TWIST


title: B16F10 cells,  ΔUNG_2, DMSO, 48h, bio replicate 2

description:
Library name: CRRA220040009-1a
Column name in all genes fpkm value.xlsx: CB_4


title: Blood, Control, White, Patient 91

description:
Library name: Patient_91
TWIST


title: Blood, Control, White, Patient 99

description:
Library name: Patient_99
TWIST


title: Blood, Control, White, Patient 89

description:
Library name: Patient_89
TWIST


title: B16F10 cells, cas9 control, DMSO, 48h, bio replicate 1

description:
Library name: CRRA220040006-1a
Column name in all genes fpkm value.xlsx: CB_1


title: 5xFAD 6, Fucose diet

city: Sacramento

first: Jacopo

last: Di Lucente

state: CA

institute: UC Davis

description: Library name: 5xFAD Fucose Diet 6

data_processing:
Glaxy version 24.0.3
Sequence reads were trimmed Trimmomatic (version 0.39)
Trimmed reads were allign to mm10 using HISAT2 (version 2.2.1)
Gene expression was measured using featureCounts (version 2.0.3)
Differentially expressed features were determined using DESeq2 (version 2.11.40.8)
Assembly: mm10
Supplementary files format and content: Normalized counts

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy plus universal mini kit (quiagen)
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Following is the workflow of library construction. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Brain

value: 1 month Fucose diet


title: Blood, Control, White, Patient 88

description:
Library name: Patient_88
TWIST


title: Blood, Control, White, Patient 86

description:
Library name: Patient_86
TWIST


title: Blood, Control, White, Patient 85

description:
Library name: Patient_85
TWIST


title: 5xFAD 4, Fucose diet

description: Library name: 5xFAD Fucose Diet 4


title: 5xFAD 5, Fucose diet

description: Library name: 5xFAD Fucose Diet 5


title: Blood, Control, White, Patient 87

description:
Library name: Patient_87
TWIST


title: Blood, Control, White, Patient 93

description:
Library name: Patient_93
TWIST


title: 5xFAD 2, Fucose diet

description: Library name: 5xFAD Fucose Diet 2


title: 5xFAD 3, Fucose diet

description: Library name: 5xFAD Fucose Diet 3


title: Blood, Control, White, Patient 83

description:
Library name: Patient_83
TWIST


title: Blood, Control, White, Patient 84

description:
Library name: Patient_84
TWIST


title: Blood, Control, White, Patient 82

description:
Library name: Patient_82
TWIST


title: 5xFAD 6, Control diet

description: Library name: 5xFAD Control Diet 6

value: 1 month Control diet


title: 5xFAD 1, Fucose diet

description: Library name: 5xFAD Fucose Diet 1


title: Blood, Control, White, Patient 81

description:
Library name: Patient_81
TWIST

value: White


title: Blood, Control, White, Patient 80

description:
Library name: Patient_80
TWIST


title: 5xFAD 5, Control diet

description: Library name: 5xFAD Control Diet 5


title: 5xFAD 2, Control diet

description: Library name: 5xFAD Control Diet 2


title: Blood, Control, White, Patient 79

description:
Library name: Patient_79
TWIST


title: Blood, Control, White, Patient 77

description:
Library name: Patient_77
TWIST


title: 5xFAD 4, Control diet

description: Library name: 5xFAD Control Diet 4


title: WT 6, Control diet

description: Library name: WT Control Diet 6


title: Blood, Control, White, Patient 75

description:
Library name: Patient_75
TWIST


title: WT 5, Control diet

description: Library name: WT Control Diet 5


title: WT 4, Control diet

description: Library name: WT Control Diet 4


title: Blood, Control, White, Patient 74

description:
Library name: Patient_74
TWIST


title: 5xFAD 1, Control diet

description: Library name: 5xFAD Control Diet 1


title: Blood, Control, White, Patient 76

description:
Library name: Patient_76
TWIST


title: Blood, Control, White, Patient 73

description:
Library name: Patient_73
TWIST


title: Blood, Control, White, Patient 71

description:
Library name: Patient_71
TWIST


title: WT 2, Control diet

description: Library name: WT Control Diet 2


title: WT 1, Control diet

description: Library name: WT Control Diet 1


title: Blood, Control, White, Patient 72

description:
Library name: Patient_72
TWIST


title: Blood, Control, White, Patient 70

description:
Library name: Patient_70
TWIST


title: Blood, Control, White, Patient 69

description:
Library name: Patient_69
TWIST


title: AE9a-Ddit4-/-  leukemia cells, rep2

city: Tianjin

first: Yishuang

last: Li

address: 288 Nanjing Road, Tianjin 300020, P. R. China

institute: State Key Laboratory of Experimental Hematology

data_processing:
CLC Genomics Workbench v 11.0.1
The data we submitted are clean data. Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Qualty limit:0.05)
Trimmed sequence reads were mappedto GrcM38/mm10 using CLC genomic benchwork (parameters- mismath cost:2 inseion cost: 3 deletion cost: 3 length fraction. 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: bone marrow

growth_protocol: Leukemia cells were maintained in IMDM with 10% FBS.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared with the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina.

treatment_protocol: HSPCs of Ddit4+/+ and Ddit4-/- mice were used and AE9a-induced leukemia models were established. Same numbers of AE9a-Ddit4+/+ and AE9aDdit4-/- GFP⁺ leukemia cells were transplanted into sub-irradiated recipients respectively.We performed global gene expression profiling by RNA sequencing on AE9a-Ddit4+/+ and AE9a-Ddit4-/leukemia cells.

value: bone marrow

tag: strain

value: leukemia cells

tag: library type

value: mRNA


title: AE9a-Ddit4-/-  leukemia cells, rep3

tag: tissue


title: Blood, Control, White, Patient 68

description:
Library name: Patient_68
TWIST

value: Control


title: Blood, Control, White, Patient 67

description:
Library name: Patient_67
TWIST


title: AE9a-Ddit4-/-  leukemia cells, rep1


title: AE9a-Ddit4+/+  leukemia cells, rep3


title: 5xFAD 3, Control diet

description: Library name: 5xFAD Control Diet 3


title: Blood, Control, White, Patient 78

description:
Library name: Patient_78
TWIST


title: Blood, Control, White, Patient 66

description:
Library name: Patient_66
TWIST


title: Blood, Control, White, Patient 65

description:
Library name: Patient_65
TWIST


title: Δfgkmt6, ChIP-seq input

description: Library name: Inp_60mM_6

organism: Fusarium graminearum

tag: cell line

value: Vegetative mycelium

value: none (input)


title: AE9a-Ddit4+/+  leukemia cells, rep1

tag: cell type


title: Blood, Control, White, Patient 64

description:
Library name: Patient_64
TWIST


title: WT 3, Control diet

description: Library name: WT Control Diet 3

tag: treatment


title: FolKmt6c_CC, ChIP-seq input

description: Library name: Inp_60mM_5


title: FolKmt6b_CC, ChIP-seq input

description: Library name: Inp_60mM_4


title: Blood, Control, White, Patient 62

description:
Library name: Patient_62
TWIST


title: Blood, Control, White, Patient 61

description:
Library name: Patient_61
TWIST


title: FolKmt6a_CC, ChIP-seq input

description: Library name: Inp_60mM_3


title: Blood, Control, White, Patient 60

description:
Library name: Patient_60
TWIST


title: FgKmt6_C, ChIP-seq input

description: Library name: Inp_60mM_2


title: Blood, Control, White, Patient 57

description:
Library name: Patient_57
TWIST


title: FgWT, ChIP-seq input

description: Library name: Inp_60mM_1

value: FgWT


title: Blood, Control, White, Patient 58

description:
Library name: Patient_58
TWIST

value: Blood


title: Δfgkmt6, ChIP-seq H3K27me3

description: Library name: Fg_60mM_6


title: FolKmt6c_CC, ChIP-seq H3K27me3

description: Library name: Fg_60mM_5


title: Blood, Control, White, Patient 56

description:
Library name: Patient_56
TWIST


title: FolKmt6b_CC, ChIP-seq H3K27me3

description: Library name: Fg_60mM_4


title: AE9a-Ddit4+/+  leukemia cells, rep2


title: Blood, Control, White, Patient 55

description:
Library name: Patient_55
TWIST


title: FolKmt6a_CC, ChIP-seq H3K27me3

description: Library name: Fg_60mM_3


title: Blood, Control, White, Patient 53

description:
Library name: Patient_53
TWIST


title: FgKmt6_C, ChIP-seq H3K27me3

description: Library name: Fg_60mM_2


title: Blood, Control, White, Patient 63

description:
Library name: Patient_63
TWIST


title: Blood, Control, White, Patient 54

description:
Library name: Patient_54
TWIST


title: Blood, PAD, White, Patient 52

description:
Library name: Patient_52
TWIST

value: PAD


title: Blood, PAD, White, Patient 51

description:
Library name: Patient_51
TWIST


title: P21Bj3_TRAP

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 271E Christopher S. Bond Life Sciences Center

institute: University of Missouri at Columbia

description: Library name: Sample 12

data_processing:
Quality check with FastQC version 0.11.9
Adapter trimming with FastP version 0.23.1
Read alignment with STAR 2.7.4a
Gene expression counts generated with HTSeq version 0.14
Assembly: Wm82.a4.v1
Supplementary files format and content: Tab-delimited text files including raw gene counts for each sample
Library strategy: TRAP-seq

organism: Glycine max

source_name: Phloem

growth_protocol: Seeds of cultivar Williams 82 of soybean (Glycine max) were surface sterilized, germinated, and grown in vermiculite: perlite soil mixture (3:1) or germination paper in a growth chamber with a 16-h light and 8-h dark photoperiod, set to 23°C during the dark and 26°C during the light regime at 80 % humidity.

extract_protocol:
TRAP was modified based on the method by (Zanetti et al., 2005) as described previously (Castro‐Guerrero et al., 2016). The optimized protocol required 10 g of root material per sample when using phloem-specific HisFLAG-GmRPL18 expressing hairy root. This was sufficient to obtain at least 500 ng of mRNA for library preparation and subsequent RNA sequencing. In this study, three biological replicates were prepared for each time point (72hr and 21day) for each treatment (mock- and B. japonicum-inoculated).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The plants were inoculated with B. japonicum strain USDA110.We used wild-type B. japonicum USDA110 for each experiment. B. japonicum cells were grown at 30°C for 3 days in HM medium (Cole and Elkan, 1973) with the appropriate antibiotics. After three days of culture, bacteria were pelleted, washed twice with sterilized deionized (DI) water, and diluted to an OD600 of 1.0 for inoculation in sterilized DI water. Plants were supplied with B&D (Broughton and Dilworth) (Broughton and Dilworth, 1971) with no nitrogen nutrient solution or with 0.5 mM NH4NO3 as in non-infected experiments.

value: Phloem

value: Treated with Bj for 21 d


title: P21Bj2_TRAP

description: Library name: Sample 11


title: FgWT, ChIP-seq H3K27me3

description: Library name: Fg_60mM_1


title: P21Bj1_TRAP

description: Library name: Sample 10


title: Blood, PAD, White, Patient 49

description:
Library name: Patient_49
TWIST

source_name: Blood

value: Female


title: Blood, PAD, White, Patient 50

description:
Library name: Patient_50
TWIST


title: P21M3_TRAP

description: Library name: Sample 9

value: Mock for 21 d


title: Blood, PAD, White, Patient 48

description:
Library name: Patient_48
TWIST


title: Blood, Control, White, Patient 59

description:
Library name: Patient_59
TWIST


title: Blood, PAD, White, Patient 47

description:
Library name: Patient_47
TWIST

value: Male


title: P21M2_TRAP

description: Library name: Sample 8


title: Blood, PAD, White, Patient 45

description:
Library name: Patient_45
TWIST


title: P72Bj3_TRAP

description: Library name: Sample 6

value: Treated with Bj for 72 h


title: Blood, PAD, White, Patient 43

description:
Library name: Patient_43
TWIST


title: P72Bj2_TRAP

description: Library name: Sample 5


title: P72Bj1_TRAP

description: Library name: Sample 4


title: Blood, PAD, White, Patient 44

description:
Library name: Patient_44
TWIST


title: P72M3_TRAP

description: Library name: Sample 3

value: Mock for 72 h


title: P72M2_TRAP

description: Library name: Sample 2


title: Blood, PAD, White, Patient 41

description:
Library name: Patient_41
TWIST

value: White


title: Blood, PAD, White, Patient 42

description:
Library name: Patient_42
TWIST


title: P72M1_TRAP

description: Library name: Sample 1


title: Blood, PAD, White, Patient 38

description:
Library name: Patient_38
TWIST


title: bm_CART

city: Changsha

first: Liwen

last: Wang

state: Hunan

address: 138 Tongzipo road

department: Department of Hematology

institute: Third Xiangya Hospital, Central South University

description: Library name: sample2

data_processing:
The raw FASTQ files were subjected to quality control, read alignment, and feature quantification using the pipeline provided by DNBC4Tools (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Before using the Ficoll lymphocyte separation liquid, the liquid is needed to be fully equilibrated at a compromise temperature of 18ºC to 20°C (room temperature) to give optimal results. Before using the Ficoll lymphocyte separation liquid, mix the liquid thoroughly by pipetting up and down. Add 3 mL Ficoll lymphocyte separation media to a 15 mL centrifuge tube. Add 2 mL whole blood containing anticoagulant (in which EDTA is recommended, heparin is prohibited) into the 15 mL centrifuge tube. Add an equal volume of 1X PBS to blood and mix gently with pipette. Carefully layer the diluted blood sample (4 mL) onto the Ficoll lymphocyte separation liquid. Centrifuge at 400g and 18 to 20℃ for 30 mins with no break. After centrifugation, there will be 4 layers, from top to bottom: blood plasma and platelets, a layer of mononuclear cells, the Ficoll lymphocyte separation medium followed by a pellet at the very bottom which contains granulocytes and erythrocytes (red blood cells). After centrifugation, the upper layer containing plasma and platelets is removed using a sterile pipette. The mononuclear cell layer is transferred to a 15 mL sterile centrifuge tube using a sterile pipette. Add 3 volumes of 1×PBS to the lymphocyte layer and carefully mix by pipetting up and down. Centrifuge at 400g and 18 to 20℃ for 10 mins and discard the supernatant. When remove platelets, centrifugation at 60g and 18 to 20℃ for 10 mins can be used. Add 6mL of 1×PBS to the lymphocyte layer and carefully mix by pipetting up and down. Centrifuge at 400g and 18 to 20℃ for 10 mins and discard the supernatant. Resuspend cells in desired volume of 1×PBS. Cell viability is examined via trypan blue staining.
The cell ( nuclear ) suspension was stained with 0.4 % trypan blue or AOPI, examine and count the viability, aggregation rate, background debris rate, and the integrity of the cell nuclei under a microscope. Once the quality control is passed, the library construction process can be initiated. Sequentially add the prepared single-cell suspension, oil, and beads to the C4 scRNA slide, and the water-in-oil droplets were prepared by DNBelab C-TaiM 4. The process of cell lysis and mRNA capture by magnetic beads was completed in the droplets. The cDNA is generated through reverse transcription using captured mRNA as template. Add the demulsification reagent into the synthesized cDNA products. After incubation at room temperature, the reaction mix is sent to centrifugation so that the cDNA product solution can be separated. After centrifugation, the cDNA product solution is extracted with pipetting. Then magnetics beads are used to enrich the cDNA products and separate out the captured short oligos from the cDNA products. Prepare a cDNA amplification reaction system to further amplify the cDNA product from the RT reaction. The cDNA amplification reaction is incubated at the appropriate temperature for a certain period. After the amplification reaction, purify the amplified cDNA product. The amplified cDNA product is quality-controlled for concentration and fragment distribution. The captured short oligos that are used to prepare the oligo library. First, prepare an amplification reaction system to further amplify the captured short oligos at an appropriate temperature for a certain period. After the oligo amplification reaction, the amplified oligo product is added with index sequence. Purify the oligo carrying the added index sequence as the oligo library which will be circularized later. The amplified cDNA products are fragmented, followed with end repairing and A-tailing.  After the A-tailing reaction, the A-tailed cDNA product is purified. A ligation reaction mix is prepared with the A-tailed cDNA fragments, adaptor sequence, reaction buffer and enzyme. The ligation reaction is set to incubate at an appropriate temperature with a certain period to ligate the adaptor sequence. After the ligation reaction, the products are purified. Prepare a PCR reaction system to amplify the final cDNA library products. The PCR reaction is set to react at an appropriate temperature for a certain number of cycles. After the PCR reaction, the final cDNA library product is purified. Choose the appropriate detection method according to product requirements for library quality control. The cDNA library and oligo library products are denatured into single strand linear DNA molecules and then circularized to be single-stranded circular products respectively. Any linear DNA molecules will be digested. Single-stranded circular DNA molecules are amplified through rolling circle amplification to form a DNA nanoball (DNB) containing multiple copies. The resulting DNBs are added to a flow cell chip with high-density patterned array technology and sequenced using combinatorial probe-anchor synthesis (cPAS) technology.

value: Bone marrow

value: CAR-T cell


title: CART_cd161_2

description: Library name: sample4

data_processing:
Raw FASTQ files were trimmed and filtered by Fastp (version 0.19.5), and then aligned to the reference genome using Bowtie2 (version 2.4.1).
The reads were counted by FeatureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts for total sample

source_name: CAR-T cell

extract_protocol:
Total RNA was extracted using the RNA rapid extraction kit (RNAfast200, Cat#220011) for RNA sequencing
Transcriptome sequencing was performed on the DNBSEQ platform with paired-end (PE150) cycles

value: Anti-CD161 mAb


title: CART_cd161_1

description: Library name: sample3


title: pb_CART

description: Library name: sample1

source_name: Peripheral blood

value: Peripheral blood


title: Blood, PAD, White, Patient 36

description:
Library name: Patient_36
TWIST


title: Blood, PAD, White, Patient 37

description:
Library name: Patient_37
TWIST


title: Blood, PAD, White, Patient 39

description:
Library name: Patient_39
TWIST


title: Blood, PAD, White, Patient 35

description:
Library name: Patient_35
TWIST


title: Blood, PAD, White, Patient 40

description:
Library name: Patient_40
TWIST


title: CART_iso_2

description: Library name: sample2

value: isotype Ab


title: P21M1_TRAP

description: Library name: Sample 7


title: Blood, PAD, White, Patient 34

description:
Library name: Patient_34
TWIST


title: 20240817-LC-6_BC28

city: Beijing

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

description: RNA-seq of  homo sapiens: lung cancer patient's plasma; Provided by Beijing chest hospital capital medical university.

data_processing:
Adapt cut  fastq files were merged by reverse R1 file using seqtk  merge. The combine files were sequentially mapped to human transcriptome by STAR STAR_2.5.3a_modified (parameters: —outSAMmultNmax 1 --outSAMtype BAM Unsorted): spike-in, univec, rRNA, MT_rRNA, MT_mRNA, MT_tRNA, chrM.all, mRNA, lncRNA, pseudogene, tRNA,srpRNA, snoRNA,snRNA, Y_RNA, misc_RNA, tucpRNA, exon, intron, intergenic
feature were summarized by featurecounts.
Assembly: hg38

source_name: plasma

extract_protocol:
Peripheral whole blood samples were collected from individuals before therapy or surgery using EDTA-coated vacutainer tubes. Plasma was separated within 2 hr after collection by centrifuge at 1,900 g for 10 min at 4 ℃. All plasma samples were aliquoted and stored at -80°C. CfRNAs were extracted using QIAzol Lysis Reagent (QIAGEN, Beijing, China), and DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China). End repair and polyadenylation were performed using E. coli Poly(A) Polymerase (NEB, Beijing, China), and T4 Polynucleotide Kinase (NEB, Beijing, China).
Reverse transcription and libraries were prepared according to DETECTOR-seq protocol with minor modifications by replacing original TSO with uracil-containing TSO and extra digestion with Uracil-DNA Glycosylase (NEB, Beijing, China) after reverse transcription. Library quantification was performed by Qubit dsDNA HS Kit. Library fragment size and quality were checked using Agilent 2100 Bioanalyzer. Libraries were sequenced on MGI Tech DNBSEQ-T7 with PE150.

value: plasma

tag: condition

value: Cancer


title: 20240817-LC-6_BC20


title: Blood, PAD, White, Patient 33

description:
Library name: Patient_33
TWIST

value: Blood


title: Blood, PAD, White, Patient 46

description:
Library name: Patient_46
TWIST

value: PAD


title: 20240817-LC-6_BC19

value: Benign


title: 20240817-LC-6_BC18


title: Blood, PAD, White, Patient 32

description:
Library name: Patient_32
TWIST


title: Blood, PAD, White, Patient 31

description:
Library name: Patient_31
TWIST


title: Blood, PAD, White, Patient 30

description:
Library name: Patient_30
TWIST


title: 20240817-LC-5_BC30


title: Blood, Control, White, Patient 28

description:
Library name: Patient_28
TWIST

value: Control


title: 20240817-LC-5_BC27


title: 20240817-LC-5_BC26


title: Blood, Control, White, Patient 27

description:
Library name: Patient_27
TWIST

value: Female


title: 20240817-LC-5_BC24


title: Blood, Control, White, Patient 29

description:
Library name: Patient_29
TWIST


title: Blood, Control, White, Patient 26

description:
Library name: Patient_26
TWIST


title: 20240817-LC-4_BC23


title: 20240817-LC-4_BC22


title: Blood, Control, White, Patient 24

description:
Library name: Patient_24
TWIST


title: CART_iso_1

description: Library name: sample1


title: 20240817-LC-4_BC21


title: Blood, Control, White, Patient 25

description:
Library name: Patient_25
TWIST


title: 20240817-LC-4_BC29


title: 20240817-LC-3_BC25


title: 20240627-LC-4_BC36


title: Blood, Control, White, Patient 20

description:
Library name: Patient_20
TWIST


title: Blood, PAD, White, Patient 19

description:
Library name: Patient_19
TWIST


title: 20240627-LC-4_BC32


title: Blood, PAD, White, Patient 22

description:
Library name: Patient_22
TWIST


title: 20240627-LC-3_BC34


title: 20240627-LC-2_BC33


title: Blood, PAD, White, Patient 16

description:
Library name: Patient_16
TWIST


title: 20240627-LC-2_BC37


title: Blood, PAD, White, Patient 17

description:
Library name: Patient_17
TWIST


title: 20240627-LC-3_BC31


title: Blood, PAD, White, Patient 15

description:
Library name: Patient_15
TWIST


title: 20240320-LC-6_BC35


title: Blood, Control, White, Patient 13

description:
Library name: Patient_13
TWIST


title: Blood, PAD, White, Patient 12

description:
Library name: Patient_12
TWIST


title: 20240627-LC-1_BC35


title: Blood, PAD, White, Patient 14

description:
Library name: Patient_14
TWIST


title: Blood, PAD, White, Patient 23

description:
Library name: Patient_23
TWIST


title: 20240320-LC-6_BC17


title: 20240320-LC-5_BC38


title: Blood, Control, White, Patient 10

description:
Library name: Patient_10
TWIST


title: Blood, PAD, White, Patient 11

description:
Library name: Patient_11
TWIST


title: Blood, PAD, White, Patient 21

description:
Library name: Patient_21
TWIST


title: 20240320-LC-5_BC33


title: 20240320-LC-5_BC22


title: 20240320-LC-6_BC21


title: Blood, PAD, White, Patient 9

description:
Library name: Patient_9
TWIST


title: Blood, Control, White, Patient 7

description:
Library name: Patient_7
TWIST


title: Blood, Control, White, Patient 6

description:
Library name: Patient_6
TWIST


title: Blood, Control, White, Patient 5

description:
Library name: Patient_5
TWIST


title: 20240320-LC-4_BC39


title: 20240320-LC-5_BC19


title: 20240320-LC-5_BC20


title: Blood, Control, White, Patient 4

description:
Library name: Patient_4
TWIST


title: 20240320-LC-4_BC26


title: Blood, Control, White, Patient 3

description:
Library name: Patient_3
TWIST


title: 20240320-LC-4_BC24


title: Blood, Control, White, Patient 1

description:
Library name: Patient_1
TWIST


title: 20240320-LC-3_BC40


title: Blood, Control, White, Patient 8

description:
Library name: Patient_8
TWIST


title: 20240320-LC-5_BC25


title: R1 tumor, black area

city: Milano

first: Francesca

last: Genova

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospedale San Raffaele

description: Library name: R1black

data_processing:
Base calling was performed on Illumina NovaSeq 6000 and sequencing adapters were removed with Trimmomatic vs 0.39
Reads were mapped to the human genome assembly GRCh38 with STAR aligner vs 2.5.3a
featureCounts vs 1.6.4 was used to annotate the genomic features with the last Genecode release (44)
Differential gene expression analysis was performed with DESeq2 package vs 1.42.1 in R/Bioconductor environment
Assembly: hg38
Supplementary files format and content: tab delimited text file of raw counts

source_name: Kidney Tumor Biopsy

extract_protocol:
Total RNA was purified from biopsies using QIAGEN AllPrep DNA/RNA Micro kit. Nucleic acids integrity was assessed with TapeStation (Agilent technologies 4200) and 0.48ng-20ng were used to prepare the library.
RNA-seq libraries were prepared using the "Low_Input_mRNA_Novaseq6000_Gb" protocol and sequenced as 100 nt single-end reads on the NovaSeq 6000 platform (Illumina)

value: Kidney Tumor Biopsy

value: VHL

tag: tumor id

tag: tumor area

value: black


title: R1 tumoe, blue area

description: Library name: R1blue

value: blue


title: 20240320-LC-3_BC37


title: 20240320-LC-3_BC30


title: L3 tumor, green area

description: Library name: L3green

value: green


title: 20240320-LC-2_BC36


title: 20240320-LC-3_BC29


title: L3 tumoe, blue area

description: Library name: L3blue


title: Blood, PAD, White, Patient 18

description:
Library name: Patient_18
TWIST

value: White

value: Male


title: L3 tumor, black area

description: Library name: L3black


title: 20240320-LC-4_BC31


title: L1 tumor, green area

description: Library name: L1green


title: L3 tumor, brown area

description: Library name: L3brown

value: brown


title: 20240320-LC-2_BC34


title: 20240320-LC-2_BC16


title: L1 tumor, brown area

description: Library name: L1brown


title: Blood, Control, White, Patient 2

description:
Library name: Patient_2
TWIST


title: L1 tumoe, blue area

description: Library name: L1blue


title: 20240320-LC-1_BC32


title: L1 tumor, black area

description: Library name: L1black


title: R1 tumor, green area

description: Library name: R1green


title: R1 tumor, brown area

description: Library name: R1brown


title: 20240320-LC-1_BC28


title: 20240320-LC-4_BC23


title: 20240113-LC-8_BC14


title: 20240320-LC-1_BC18


title: 20240320-LC-4_BC15


title: A673, 48hr, Compound 20 2uM, rep3

city: Columbus

first: John

middle: William

last: Sherman

state: Ohio

address: 575 Childrens Crossroads

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description:
Library name: CMPD_20_3
Column name in geo_counts.csv: CMPD_20_3

data_processing:
trim-galore (0.6.7) Parameters: --fastqc --paired
star (2.7.9a) Parameters: --readFilesCommand zcat --twopassMode Basic --outSAMtype BAM Unsorted SortedByCoordinate --sjdbGTFfile {annotation} --genomeLoad NoSharedMemory --quantMode GeneCounts
samtools (1.13) Pipe: collate -Ou | fixmate -mu | sort -u | markdup -s
featurecount (subread 2.0.6) Parameters: -p --countReadPairs -a {annotation} -t exon -g gene_id --ignoreDup
Assembly: Hg38
Supplementary files format and content: geo_counts.csv Format: featurecount output converted to CSV, Content: All samples associated with this GEO submission
Supplementary files format and content: accession_counts.csv Format: featurecount output converted to CSV, Content: samples from this submission,  combined with select samples from GSE94502 and GSE98787 including associated sample accession numbers on the second line.
Supplementary files format and content: counts.csv Format: direct featurecount output (TSV), Content: All samples from this GEO submission combined with select samples from GSE94502 and GSE98787 as used for down stream analysis

growth_protocol: Cells were cultured in DMEM high-glucose + 10% Fetal Bovine Serum + 1% Penicilin/Streptomycin/Glutamine supplement + 1% Sodium Pyruvate supplement in 5% CO2 at 37 degrees C

extract_protocol:
RNA was extracted by Qiagen Rneasy
NEBNext Ultra II Directional kit was used according to manufacturer instructions

treatment_protocol: Treatment was added 48 hours prior to harvest

value: Ewing Sarcoma

tag: genotype

value: WT

value: Compound 20 2uM


title: A673, 48hr, OG-L002 2uM, rep2

description:
Library name: OGL_2
Column name in geo_counts.csv: OGL_2

value: OG-L002 2uM


title: 20240113-LC-8_BC13

value: plasma


title: A673, 48hr, OG-L002 2uM, rep1

description:
Library name: OGL_1
Column name in geo_counts.csv: OGL_1


title: A673, 48hr, OG-L002 2uM, rep3

description:
Library name: OGL_3
Column name in geo_counts.csv: OGL_3


title: 20240113-LC-7_BC12

value: Cancer


title: 20240113-LC-7_BC11

value: Benign


title: C2-/-_3, 5-6 months old

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

description: Library name: KO3

data_processing:
The raw data containing reads of low quality, connector contamination and excessively high leveles of unknown base N were removed before data analysis. The clean reads thus generated were aligned to the reference genome using HISAT. The quantification of raw gene counts was carried out through the utilization of feature Counts (v1.5.2) (15), and subsequent normalization was achieved by applying edgeR's TMM (trimmed mean of M values) method. To identify differentially expressed genes (DEGs), we employed the limma/voom approach.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Supplementary files format and content: The processed file is in Excel format and contains TMM of individual genes.
Supplementary files format and content: Supplementary files format and content: The processed file is in Excel format and containsgene name log2fc,average expression, pvalue,adjP value for the respetive genes.

source_name: Tibialis anterior muscle

growth_protocol: C2-/- mice and FVBN WT male mice were grown upto 5-6 months of age and used for experiments in this work. The animal facility had a controlled environment (20°C temperature, 60% humidity, and 12 hours of light/dark cycles), and mice were fed ad libitum with a standard diet.

extract_protocol:
TA muscles were dissected at 5-6 months of age, followed by total RNA isolation using an RNA isolation kit (Qiagen, cat# 763134), according to the manufacturer’s instructions. Total RNA concentration and quality (A260/280 ratio ≥2.0) were evaluated using a Nanodrop spectrophotometer (ThermoFisher Scientific). The quality of total RNA was further measured using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
After Sample QC was by qubit and Agilent Bioanalyzer, a certain amount of RNA samples were denatured at suitable temperatures to open-up their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads followed by mRNA fragmentation and cDNA Synthesis. The double-stranded cDNA fragments were subjected to end-repair, the addition of a single ‘A’ nucleotide to the 3’ ends of the blunt fragments and ligated to adaptors before amplification. After quality control of the prepared library, the amplified products were denatured to generate single stranded PCR products which was then circularized to replicate using rolling cycle amplification yielding a DNA nanoball (DNB) containing multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Tibialis anterior muscle

tag: age


title: A673, 48hr, Compound 20 2uM, rep2

description:
Library name: CMPD_20_2
Column name in geo_counts.csv: CMPD_20_2


title: C2-/-_2, 5-6 months old

description: Library name: KO2


title: C2-/-_1, 5-6 months old

description: Library name: KO1


title: A673, 48hr, Compound 19 2uM, rep2

description:
Library name: CMPD_19_2
Column name in geo_counts.csv: CMPD_19_2

value: Compound 19 2uM


title: A673, 48hr, Compound 20 2uM, rep1

description:
Library name: CMPD_20_1
Column name in geo_counts.csv: CMPD_20_1


title: A673, 48hr, Compound 19 2uM, rep1

description:
Library name: CMPD_19_1
Column name in geo_counts.csv: CMPD_19_1


title: A673, 48hr, Compound 15 2uM, rep3

description:
Library name: CMPD_15_3
Column name in geo_counts.csv: CMPD_15_3

value: Compound 15 2uM


title: A673, 48hr, Compound 15 2uM, rep2

description:
Library name: CMPD_15_2
Column name in geo_counts.csv: CMPD_15_2


title: WT_4, 5-6 months old

description: Library name: WT4

value: FVBN/WT


title: A673, 48hr, Compound 19 2uM, rep3

description:
Library name: CMPD_19_3
Column name in geo_counts.csv: CMPD_19_3


title: WT_1, 5-6 months old

description: Library name: WT1


title: WT_2, 5-6 months old

description: Library name: WT2


title: C2-/-_4

description: Library name: KO4

data_processing:
The raw data containing reads of low quality, connector contamination and excessively high leveles of unknown base N were removed before data analysis. The clean reads thus generated were aligned to the reference genome using HISAT, mapped to reference genes using Bowtie2. The mapped genes were  subjected to differential expression analysis using DEseq2. The nondiabetic samples were grouped as control-2 and the diabetic samples were  grouped as case-2 for the DESeq2 analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: The processed file is in Excel format and contains FPKM, TPM, read counts, log2fc, qvalue, p value for the respetive genes with their gene symbol, gene ID and other gene related informations.

growth_protocol: C2-/- mice and FVBN WT male mice were grown upto 2 months of age and used for experiments in this work. The animal facility had a controlled environment (20°C temperature, 60% humidity, and 12 hours of light/dark cycles), and mice were fed ad libitum with a standard diet.

extract_protocol:
TA muscles were dissected at 22 months of age, followed by total RNA isolation using an RNA isolation kit (Qiagen, cat# 763134), according to the manufacturer’s instructions. Total RNA concentration and quality (A260/280 ratio ≥2.0) were evaluated using a Nanodrop spectrophotometer (ThermoFisher Scientific). The quality of total RNA was further measured using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
After Sample QC was by qubit and Agilent Bioanalyzer, a certain amount of RNA samples were denatured at suitable temperatures to open-up their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads followed by mRNA fragmentation and cDNA Synthesis. The double-stranded cDNA fragments were subjected to end-repair, the addition of a single ‘A’ nucleotide to the 3’ ends of the blunt fragments and ligated to adaptors before amplification.
After quality control of the prepared library, the amplified products were denatured to generate single stranded PCR products which was then circularized to replicate using rolling cycle amplification yielding a DNA nanoball (DNB) containing multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: 22 Months


title: A673, 48hr, Compound 15 2uM, rep1

description:
Library name: CMPD_15_1
Column name in geo_counts.csv: CMPD_15_1


title: A673, 48hr, DMSO 0.1%, rep3

description:
Library name: DMSO_3
Column name in geo_counts.csv: DMSO_3

value: DMSO 0.1%


title: A673, 48hr, DMSO 0.1%, rep2

description:
Library name: DMSO_2
Column name in geo_counts.csv: DMSO_2


title: C2-/-_2

description: Library name: KO2


title: C2-/-_3

description: Library name: KO3


title: A673, 48hr, DMSO 0.1%, rep1

description:
Library name: DMSO_1
Column name in geo_counts.csv: DMSO_1


title: C2-/-_1

description: Library name: KO1


title: Wildtype_4

description: Library name: WT4


title: Wildtype_3

description: Library name: WT3


title: Wildtype_2

description: Library name: WT2


title: Wildtype_1

description: Library name: WT1


title: TILs WIOG Day14_2

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

country: South Korea

institute: CHA Bundang Medical Center

description:
D14 WIOG_SC253
Day 14 WIOG TILs-rep2

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (hg19) using HISAT v2.1.0 (KIM et al, 2015) and then, transcript assembly of known transcripts was processed by StringTie v1.3.4d (Pertea, Mihaela, et al., 2015, 2016).
Based on the result of that, expression abundance of transcript and gene were calculated as read count or TPM value per sample.
The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes).
WIOG The fold change was calculated between WIO group and WIOG group. The statistical significances were calculated using ANOVA
Assembly: The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from the NCBI.
Supplementary files format and content: FPKM, TPM values of genes for 6 samples, 3 from day 14 WIO and 3 from day 14.

source_name: Tumor infiltrating lymphocyte

growth_protocol: Following tumor processing, single cells were cultured in complete medium (CM) for 14 days. CM for culturing TILs consisted of 1:1 mixture of RPMI1640 medium with GlutaMAX (Gibco) supplemented with 10% human serum albumin (Sigma Aldrich, St.Louis, MO, USA), 100 U/ mL penicillin and 100 μg/mL streptomycin (Gibco), 55µM 2-mercaptoethanol (Gibco) and AIM-V medium (Gibco).

extract_protocol:
RNA of sorted cells at Day 0 and Day 14 was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
In order to construct cDNA libraries, we used the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., San Diego, CA, USA). The protocol comprised polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription, and 100 nt paired-end sequencing using Illumina NovaSeq 6000 (Illumina, Inc)

treatment_protocol: TILs were expanded in four conditions with IL-2 (Peprotech, Cranbury, NJ, USA): (1) control (W group), (2)anti-PD1 antibody (WI group), (3) anti-PD1 antibody + IL-15 + IL-21 (WIO group), (4) anti-PD1 antibody + IL-15 + IL-21 +anti-GITR antibody (BPS Bioscience, San Diego, CA, USA) (WIOG group).

tag: source

value: Ovarian tumor

value: Tumor infiltrating lymphocyte

tag: culture day

value: cultured with anti-GITR (WIOG group)


title: WT_3, 5-6 months old

description: Library name: WT3

value: Male


title: TILs WIOG Day14_3

description:
D14 WIOG_FSC243
Day 14 WIOG TILs-rep3


title: Hippo_AA_2

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
The resulting clean reads were saved in FASTQ format and subsequently aligned to the reference genome using HISAT2. The clean reads were aligned against the reference coding gene set using Bowtie2
Genes expression level is quantified through RSEM.
Differential expression analysis was carried out utilizing DESeq2, which identified genes with statistically significant differences at a threshold of Q < 0.05.
Assembly: GRCm38.84
Supplementary files format and content: FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: hippocampus

value: (+)-Sodium L-ascorbate


title: TILs WIO Day14_3

description:
D14 WIO_FSC243
Day 14 WIO TILs-rep3

value: cultured W/O anti-GITR (WIO group)


title: Hippo_AA_1


title: Hippo_Ctrl_2

value: PBS


title: TILs WIO Day14_2

description:
D14 WIO_SC253
Day 14 WIO TILs-rep2


title: TILs WIO Day14_1

description:
D14 WIO_SC245
Day 14 WIO TILs-rep1


title: Hippo_Ctrl_1