title: WT_24hpi

city: Paris

first: Pedro Pablo

last: HERNANDEZ CERDA

address: 11-13 rue Pierre et Marie Curie, BDD building

country: France

institute: Institut Curie

description: Library name: P148-P146T24

data_processing:
CellRanger pipeline
Assembly: danRer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Gut

extract_protocol:
10 guts from 5 dpf larvae were dissected and placed in 200 μL of a dissociation cocktail (1 mg/mL fresh collagenase A, 40 μg/mL proteinase K, and 0.25% trypsin in PBS) at 37°C for 30 minutes. 50 guts were dissected per condition for a total of 5 replicate tubes per condition. Cells were centrifuged at 300 RCF for 15 minutes at 4°C. The pellet was resuspended in 200 μL PBS with 0.04% non-acetylated BSA. Replicates were pooled and filtered through a 40 μm cell strainer (Fisherbrand, #22363547). Samples were centrifuged at 300 RCF for 15 minutes at 4°C and resuspended with in 50 ul of PBS with 0.04% non-acetylated BSA. To isolate live cells, an OptiPrep™ Density Gradient Medium (Sigma, #D1556-250ML) was used. A 40% (w/v) iodixanol working solution was prepared by mixing 2 volumes of OptiPrep™ with 1 volume of 0.04% BSA in 1X PBS/DEPC-treated water. This working solution was used to create a 22% (w/v) iodixanol solution in the same buffer. The cell suspension was mixed with one volume of the working solution and 0.45 volume of the cell suspension via gentle inversion, transferred to a 15 mL conical tube, and topped up to 6 mL with the working solution. This solution was overlaid with 3 mL of the 22% iodixanol, and then with 0.5 mL of PBS with 0.04% BSA. Samples were centrifuged at 800 RCF for 20 minutes at 20°C. Viable cells were collected from the top interface, diluted in PBS with 0.04% BSA, and centrifuged at 300 RCF for 10 minutes at 4°C. The supernatant was discarded, and the cells were resuspended in PBS with 0.04% non-acetylated BSA to reach the desired concentration. Data analysis was performed using the Seurat package in R (Hao et al, 2024).
Cells were loaded onto a 10× Chromium instrument (10× Genomics) and libraries were prepared using the Single Cell 3′ Reagent Kit (V2 chemistry) (10× Genomics) according to the manufacturer's instructions. The sequencing coverage was approximately 100,000 reads per cell

value: Gut

value: WT


title: DSP-1001660019865-E-E02

status: Public on Jul 15 2026

type: SRA

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

country: USA

institute: UT Southwestern Medical Center

description: Library name: Sample 289

library_source: transcriptomic

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw read counts in DCC
Supplementary files format and content: RNA_Q3_normalied_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

molecule: total RNA

organism: Homo sapiens

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

tag: tissue

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

tag: treatment

value: PF

tag: scan name

tag: roi

tag: segment

value: Desmin


title: H5/ALC-82-d28

type: protein

city: Irvine

first: Li

last: Liang

state: CA

address: 847 Health Sciences

institute: University of California Irvine

hyb_protocol: The microarray slides were probed with mouse sera diluted 1:100 in protein array blocking buffer (GVS Life Sciences, Sanford, ME) overnight at 4°C and washed with TTBS buffer (20mM Tris-HCl, 150mM NaCl, 0.05% Tween 20 in double-distilled water (ddH2O) adjusted to pH 7.5 and filtered) three times for 5 min each. Mouse IgG  secondary antibody conjugated to AF647, was applied to each of the microarray pads and incubated for 2 h at room temperature, and pads were then washed with TTBS three times for 5 min each and dried.

scan_protocol: The slides were imaged using an ArrayCam imager (Grace Bio-Labs). The output RGB TIFF files generated by the imager were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.

molecule: protein

organism: Mus musculus

source_name: Plasma

tag: days post prime immunization


title: THP-1 cells, MPXV lineage A.1-infected, 24h pi, replicate 3

city: London

first: Rebecca

last: Sumner

address: 2nd Floor Borough Wing, Guy's Hospital

department: Department of Infectious Diseases

country: United Kingdom

institute: King's College London

description: Library name: THPA1_3

data_processing:
RNA-seq reads were aligned to the Homo Sapiens genome using HISAT2 and featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene and the FPKM of each gene was calculated based on the length of the gene and reads count mapped to it. Differentially expressed genes (DEG) were calculated using DESeq2. The resulting P-values from DESeq2 were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: csv file includes FPKM data for each sample

source_name: PMA-differentiated THP-1

growth_protocol: HFFF2 cells were cultured in Dulbecco modified Eagle medium (Sigma) and THP-1 cells were cultured in RPMI medium (Gibco), all supplemented with 10 % foetal bovine serum (FBS, Biowest) and 100 U/mL penicillin and 100 µg/mL streptomycin (Pen/Strep; Life Technologies).

extract_protocol:
Total RNA was extracted using the RNeasy mini RNA extraction kit (QIAgen) including on-column DNase treatment according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesised using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were then pooled and sequenced on an Illumina platform.

treatment_protocol: THP-1 cells were differentiated for 48 h in the presence of 50 ng/mL PMA (Peprotech).

tag: cell line

value: PMA-differentiated THP-1

tag: cell type

value: acute monoctyic leukaemia

tag: genotype

value: THP-1 IFIT-1 Luc

value: PMA-differentiation, infected with MPXV A.1


title: DSP-1001660019865-E-E01

description: Library name: Sample 288


title: THP-1 cells, MPXV lineage A.1-infected, 24h pi, replicate 2

description: Library name: THPA1_2


title: WT_ctrl

description: Library name: P148-P146T23

library_source: transcriptomic single cell


title: LD 6mpk T 7.5mpk 5

city: San Diego

first: Aarash

last: Bordbar

address: 3210 Merryfield Row

institute: Sinopia Biosciences

data_processing:
FastQ files were quality controlled using FastQC. Reads were mapped to the Norway rat genome (Rnor_6.0.94) using STAR. Aligned reads were counted using HTseq using the “intersection_strict” mode.
Assembly: Rnor_6.0.94
Supplementary files format and content: raw_counts.txt contains the HTseq output

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
Total RNA was obtained from homogenized striatum using the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared using polyA capture and reverse transcription of cDNA

value: Striatum

tag: gender

value: female

tag: strain

value: Sprague Dawley


title: H5/ALC-81-d28


title: DSP-1001660019865-E-D12

description: Library name: Sample 287

value: CF


title: Tg(gnrh3:EGFP) zebrafish, 7 dpf, GnRH3 neuronal nuclei

city: Baltimore

first: Yalong

last: Sun

state: MD

address: 701 E Pratt Street

institute: IMET, UMBC

description:
Library name: XNZ10
10x genomics

data_processing:
Alignment, initial data processing, nuclei clustering and marker gene identification were finished using Cell Ranger software v7.1.0 (10×Genomics, Pleasanton, CA, USA) and Seurat v4.3.0 R package in R v4.2.3 environment.
Assembly: GRCz11/danRer11 (Ensembl release 106; GCA_000002035.4)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Neuronal cells

extract_protocol:
250 live larvae of Tg(gnrh3:EGFP) were euthanized by chilling on ice for 20 minutes, followed by de-yolking by vigorous pipetting with 200 µl tip using 3 mL swelling buffer (250mM Sucrose, 10mM Tris-HCL (pH 7.9), 10mM MgCl2 and 1mM EGTA). The mixture was passed through a 40 uM tube top into 50 ml falcon tube. The retained embryos were transferred to a tube containing 3.5 mL of cell lysis buffer (Nuclei EZ Lysis Buffer, Sigma) and incubated on ice for 30-40 mins, during which the solution was passed through 3 mL syringe equipped with 22-gauge needle every 5 mins. The mixture was then centrifuged at 500g at 4oC for 5 min and the supernatant was collected twice and pooled supernatant was filtered through 20 µm filter into 15 mL falcon tube. After centrifugation at 500g for 5 min at 4°C, supernatant was removed and then the pellet containing the nuclei was resuspended in 1 mL PBS+1% BSA containing 200 units/mL protector RNase inhibitor (Millipore Sigma, MD, USA). 50 ul 7-AAD stain was added, and the nuclei were then subjected to fluorescence-activated cell sorting (FACS) to enrich GnRH3 nuclei based on EGFP labeling using BD FACS Aria II cell sorters (Nozzle 100 μm)
Single-nuclei RNA sequencing (snRNA-Seq) cDNA library was prepared from 10,000 nuclei using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10×Genomics, Pleasanton, CA, USA) on the 10×Genomics Chromium Controller according to the manufacturer’s manual. cDNAs were barcoded followed by the library sequenced using Illumina NovaSeq6000 platform with 100-bp paired-end reads at a depth of 77,538 mean reads per nucleus.

value: Neuronal cells


title: THP-1 cells, MPXV lineage A.1-infected, 24h pi, replicate 1

description: Library name: THPA1_1


title: H5/DOTMA/CpG+MPLA-75-d28


title: zebrafish-birc3-het-tc-8d-3

city: Toronto

first: Aleixo

last: Muise

state: ON

address: 686 Bay Street, 19-9400 I-M PGCRL

department: Cell Biology

country: Canada

institute: The Hospital for Sick Children

description:
Library name: sample33
15_z_birc3kohet_8d_3_S39

data_processing:
Raw reads in FASTQ format were processed using Fastp (version 0.23.1) for quality control. The raw RNAseq reads were aligned to the mouse genome (GRCm39) / zebrafish genome (GRCz11) using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2.
Assembly: Mus musculus (GRCm39 genome) zebrafish (GRCz11)
Supplementary files format and content: tab-delimited text files include the count values for each Sample. Rows = genes; Columns = samples.

source_name: whole fish(with tailfin cut)

growth_protocol: For Mus Musculus: Mouse small intestinal organoids were cultured in ENR medium in an incubator at 37°C with 5% CO₂.  For Danio rerio: For wt and all the mutants at 3dpf and 8dpf ,embryos were obtained via natural mating and cultured in embryo E3 buffer, raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.

extract_protocol:
For Mus Musculus: Total RNA was extracted using TRNzol reagent (TIANGEN). 0.45μg of high-quality RNA was used for RNA-seq library construction.  For Danio rerio: RNA were extracted using RNAeasy mini kit(Qiagen). 600ng of total RNA were used for the construction of sequencing libraries.
For Mus Musculus: RNA libraries for RNA-Seq were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer’s instructions.  For Danio rerio: RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo-Zero Plus protocol to generate polyA-enriched, rRNA-depleted libraries.

treatment_protocol: For Mus Musculus: Three days after seeding in 24-well plates, the organoids were stimulated with TNF (10 ng/ml) for 15 hours.  For Danio rerio: Wt and all the mutants at 3dpf and 8dpf were anethetized with tricaine and underwent tailfin-cut genotyping.The wildtype and mutants were pooled (n=15), repectively.

value: whole fish(with tailfin cut)

value: het

value: no treatment


title: DSP-1001660019865-E-D11

description: Library name: Sample 286


title: H5/DOTMA/CpG+MPLA-74-d28


title: THP-1 cells, mock-infected, 24h pi, replicate 3

description: Library name: THPmock3

value: PMA-differentiation


title: zebrafish-wt-tc-8d-3

description:
Library name: sample32
14_z_wt_8d_3_S38

value: WT


title: DSP-1001660019865-E-D10

description: Library name: Sample 285

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: H5/DOTMA/CpG+MPLA-73-d28


title: H5/ALC/CpG+MPLA-102-d28


title: THP-1 cells, mock-infected, 24h pi, replicate 2

description: Library name: THPmock2


title: zebrafish-birc3-het-tc-8d-2

description:
Library name: sample31
13_z_birc3kohet_8d_2_S37


title: THP-1 cells, mock-infected, 24h pi, replicate 1

description: Library name: THPmock1


title: DSP-1001660019865-E-D09

description: Library name: Sample 284


title: H5/DOTMA/CpG+MPLA-71-d28


title: zebrafish-wt-tc-8d-2

description:
Library name: sample30
12_z_wt_8d_2_S36


title: SRPK2 iRIP-seq, MDA-MB-231, input replicate 1

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

country: China

institute: The Second Hospital of Dalian Medical University

description: Library name: SRPK2_Input_1

data_processing:
Illumina bcl2fastq software used for basecalling. 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.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of SPRK2 on genome using “ABLIRC” strategy.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

extract_protocol:
The SRPK2-bound RNA was isolated from the immunoprecipitation of anti-SRPK2 using Trizol (Invitrogen).
Complementary DNA (cDNA) libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according to the manufacturer’s procedure and high-throughput sequencing of the cDNA libraries was performed on an Illumina Xtenplatform for 150 bp paired-end sequencing.

value: breast cancer


title: DSP-1001660019865-E-D08

description: Library name: Sample 283

value: Desmin


title: HFFF cells, MPXV lineage B.1-infected, 24h pi, replicate 3

description: Library name: HFFFB1_3

value: primary human foetal foreskin fibroblast

value: infected with MPXV B.1


title: H5/DOTMA/CpG-65-d28


title: zebrafish-birc3-het-tc-8d-1

description:
Library name: sample29
11_z_bric3kohet_8d_1_S35


title: DSP-1001660019865-E-E07

description: Library name: Sample 294

value: PF


title: DSP-1001660019865-E-D07

description: Library name: Sample 282


title: H5/DOTMA/CpG-64-d28


title: HFFF cells, MPXV lineage B.1-infected, 24h pi, replicate 2

description: Library name: HFFFB1_2


title: zebrafish-wt-tc-8d-1

description:
Library name: sample28
10_z_wt_8d_1_S34


title: HFFF cells, MPXV lineage B.1-infected, 24h pi, replicate 1

description: Library name: HFFFB1_1


title: H5/DOTMA/CpG-63-d28


title: zebrafish-birc3-hom-tc-3d-3

description:
Library name: sample27
9_z_birc3kohomo_3d_3_S33

value: hom


title: DSP-1001660019865-E-D05

description: Library name: Sample 280


title: H5/DOTMA/CpG-62-d28


title: HFFF cells, MPXV lineage A.1-infected, 24h pi, replicate 3

description: Library name: HFFFA1_3

value: infected with MPXV A.1


title: zebrafish-birc3-het-tc-3d-3

description:
Library name: sample26
8_z_birc3kohet_3d_3_S32


title: DSP-1001660019865-E-D04

description: Library name: Sample 279


title: H5/DOTMA/CpG-61-d28


title: HFFF cells, MPXV lineage A.1-infected, 24h pi, replicate 2

description: Library name: HFFFA1_2


title: zebrafish-wt-tc-3d-3

description:
Library name: sample25
7_z_wt_3d_3_S31


title: DSP-1001660019865-E-D03

description: Library name: Sample 278


title: HFFF cells, MPXV lineage A.1-infected, 24h pi, replicate 1

description: Library name: HFFFA1_1


title: zebrafish-birc3-hom-tc-3d-2

description:
Library name: sample24
6_z_birc3kohomo_3d_2_S30


title: H5/DOTMA-55-d28


title: DSP-1001660019865-E-D02

description: Library name: Sample 277


title: HFFF cells, mock-infected, 24h pi, replicate 3

description: Library name: HFFFmock3


title: H5/DOTMA-54-d28


title: zebrafish-birc3-het-tc-3d-2

description:
Library name: sample23
5_z_birc3kohet_3d_2_S29


title: H5/DOTMA-53-d28


title: HFFF cells, mock-infected, 24h pi, replicate 2

description: Library name: HFFFmock2


title: DSP-1001660019865-E-D01

description: Library name: Sample 276


title: zebrafish-wt-tc-3d-2

description:
Library name: sample22
4_z_wt_3d_2_S28


title: HFFF cells, mock-infected, 24h pi, replicate 1

description: Library name: HFFFmock1


title: H5/DOTMA-51-d28


title: DSP-1001660019865-E-C12

description: Library name: Sample 275


title: H5/IVAX-1-Chol-45-d28


title: DSP-1001660019865-E-C11

description: Library name: Sample 274


title: WNT, 72 h, rep 2

city: Cincinnati

first: Aryeh

last: Warmflash

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description:
Library name: H72_R2
Column name in abundance_combined_W.csv: H72_R2

data_processing:
Raw sequencing reads were quantified using Salmon (v1.9.0) against the human GRCh38 transcriptome using the selective alignment method. Salmon was run with automatic library type detection (-l A) and mapping validation enabled (--validateMappings). Transcript abundance estimates were imported into R using the tximeta package and summarized to generate gene-level count matrices for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: csv file includes TPM values for each sample

growth_protocol: Cells were cultured in the chemically defined medium mTeSR1 (STEMCELL Technologies) on Matrigel-coated dishes (Corning, 1:500 in PBS) and kept at 37°C, 5% CO2. Cells were passaged using Dispase (STEMCELL Technologies; 1:5 dilution in DMEM/F12 (VWR)) and regularly tested for pluripotency and mycoplasma contamination.

extract_protocol:
Cells were dissociated with Accutase, and total RNA was extracted using the Invitrogen RNAqueous-Micro Total RNA Isolation Kit according to the manufacturer's instructions. RNA quality was assessed using a NanoDrop spectrophotometer, agarose gel electrophoresis, qPCR, and an Agilent 2100 Bioanalyzer before library preparation.
RNA sequencing libraries were prepared by Novogene Co. using a poly(A)-enriched mRNA library preparation protocol. Libraries were sequenced on the Illumina NovaSeq X Plus platform to generate paired-end 150-bp reads.

treatment_protocol: Human pluripotent stem cells were seeded at a density of 30,000 cells/cm² in 24-well plates and maintained in mTeSR1 medium supplemented with ROCK inhibitor for 24 hours before differentiation. Differentiation was initiated by replacing the medium with N2B27 containing SB (10 μM) and LDN (100 nM). Human recombinant WNT3A protein was added 34 hours after the start of differentiation. Cells were harvested at the indicated time points for RNA extraction.

value: human pluripotent stem cells

value: wild type

value: posterior neural fate differentiation

tag: time

tag: batch


title: zebrafish-birc3-hom-tc-3d-1

description:
Library name: sample21
3_z_birc3kohomo_3d_1_S27


title: zebrafish-birc3-het-tc-3d-1

description:
Library name: sample20
2_z_birc3kohet_3d_1_S26


title: Gastric MALT lymphoma Visium HD spatial transcriptomics

city: Shanghai

first: Jiadai

last: Xu

address: Xuhui District, Zhongshan Hospital Fudan University

institute: Zhongshan Hospital Fudan University

description:
Library name: LC_24G22292
Gastric MALT lymphoma FFPE tissue profiled by 10x Genomics Visium HD Spatial Gene Expression.

data_processing:
FASTQ files were generated from Illumina paired-end sequencing reads.
FASTQ files were processed with Space Ranger v3.0 using the human reference genome.
Spatial transcriptomics downstream analyses were performed using Seurat, SPOTlight, CellChat, AddModuleScore, and related R workflows as described in the manuscript.
Processed Space Ranger matrix and spatial image outputs will be supplied as supplementary processed data files before final GEO release.
Assembly: GRCh38 human reference genome used by Space Ranger v3.0. Confirm exact reference package before final submission.
Supplementary files format and content: Processed data will include Space Ranger filtered feature-barcode matrices, spatial coordinate and image files, and selected downstream annotation and result tables. LC_24G22292 processed matrix is pending transfer from another computer.
Library strategy: Spatial Transcriptomics

source_name: stomach

growth_protocol: FFPE tissue sections from MALT lymphoma biopsy samples were used for Visium HD spatial transcriptomics.

extract_protocol:
Total RNA was isolated from FFPE tissue blocks. RNA quality was assessed by DV200, and samples passing quality control were processed using the 10x Genomics Visium HD Spatial Gene Expression workflow.
FFPE tissue sections were deparaffinized, stained and imaged, followed by probe hybridization, ligation, probe release, extension, library construction, and paired-end sequencing according to the 10x Genomics Visium HD Spatial Gene Expression protocol.

treatment_protocol: No ex vivo treatment was applied to the submitted tissue sections.

value: stomach

value: MALT lymphoma tissue

value: first-line orelabrutinib plus obinutuzumab cohort; pretreatment biopsy

value: Visium HD


title: DSP-1001660019865-E-C10

description: Library name: Sample 273


title: WNT, 50 h, rep 2

description:
Library name: H50_R2
Column name in abundance_combined_W.csv: H50_R2


title: H5/IVAX-1-Chol-44-d28


title: zebrafish-wt-tc-3d-1

description:
Library name: sample19
1_z_wt_3d_1_S25

value: whole fish(with tailfin cut)

value: no treatment


title: H5/IVAX-1-Chol-43-d28


title: DSP-1001660019865-E-C09

description: Library name: Sample 272

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: WNT, 42 h, rep 2

description:
Library name: H42_R2
Column name in abundance_combined_W.csv: H42_R2


title: Mice, cNr3c1, ZT21

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

description: Library name: Mice_cNr3c1_ZT21

data_processing:
FASTQ files were obtained from the sequencing provider for each pooled WT or cKO time-point sample and uploaded to RaNAseq (https://ranaseq.eu/) for RNA-seq data processing.
Quality control, read mapping to the mouse reference genome, and generation of gene-level expression values were performed using RaNAseq.
Differentially expressed genes (DEGs) were identified using RaNAseq by comparing WT (Cre-) and retina-specific Nr3c1 cKO (Cre+) samples at the corresponding ZT time points.
Time-series expression profiles across ZT3, ZT9, ZT15, and ZT21 were then used to evaluate rhythmic gene expression patterns and genes whose rhythmicity was lost or altered in retina-specific Nr3c1 cKO samples.
Processed expression matrices, DEG analysis results, and rhythmic gene expression analysis results were generated from the RaNAseq-processed time-series RNA-seq data.
Assembly: Mus musculus reference genome; exact genome build/assembly to be confirmed based on the reference used for read mapping.
Supplementary files format and content: Processed data files contain gene-level expression values for each pooled genotype/time-point sample, DEG analysis results generated using RaNAseq, and rhythmic gene expression analysis results comparing WT and retina-specific Nr3c1 cKO samples.

source_name: ciliary body

growth_protocol: Male 12-week-old WT (Cre-) and retina-specific Nr3c1 cKO (Cre+) mice were maintained under 12 h light/12 h dark (12L:12D) conditions before sampling.

extract_protocol:
At each time point, whole eyes were collected from three WT mice and three cKO mice. Each whole-eye sample was homogenized with a pestle, and total RNA was extracted. Equal amounts of RNA from the three individuals in each genotype/time-point group were pooled for RNA-seq analysis.
RNA sequencing libraries were prepared from pooled total RNA samples for each genotype/time-point group and sequenced by an external service provider.

treatment_protocol: No drug treatment was performed. Whole eyes were collected every 6 hours at 3, 9, 15, and 21 hours after lights-on (ZT3, ZT9, ZT15, and ZT21) under 12L:12D conditions.

value: ciliary body

value: nonpigmented ciliary epithelial cell

tag: time-point


title: WNT, 34 h, rep 2

description:
Library name: H34_R2
Column name in abundance_combined_W.csv: H34_R2


title: DSP-1001660019865-E-C08

description: Library name: Sample 271

value: Desmin


title: H5/IVAX-1-Chol-42-d28


title: Mice, cNr3c1, ZT15

description: Library name: Mice_cNr3c1_ZT15


title: WNT, 72 h, rep 1

description:
Library name: H72_R1
Column name in abundance_combined_W.csv: H72_R1


title: H5/IVAX-1-Chol-41-d28


title: Mice, cNr3c1, ZT9

description: Library name: Mice_cNr3c1_ZT9


title: DSP-1001660019865-E-C07

description: Library name: Sample 270


title: DSP-1001660019865-E-C06

description: Library name: Sample 269


title: WNT, 50 h, rep 1

description:
Library name: H50_R1
Column name in abundance_combined_W.csv: H50_R1


title: H5/IVAX-1-35-d28


title: Mice, cNr3c1, ZT3

description: Library name: Mice_cNr3c1_ZT3


title: WNT, 42 h, rep 1

description:
Library name: H42_R1
Column name in abundance_combined_W.csv: H42_R1


title: H5/IVAX-1-34-d28


title: DSP-1001660019865-E-C05

description: Library name: Sample 268


title: Mice, WT, ZT21

description: Library name: Mice_WT_ZT21

value: WT


title: H5/IVAX-1-33-d28


title: WNT, 34 h, rep 1

description:
Library name: H34_R1
Column name in abundance_combined_W.csv: H34_R1


title: DSP-1001660019865-E-C04

description: Library name: Sample 267

value: CF


title: Mice, WT, ZT15

description: Library name: Mice_WT_ZT15


title: DSP-1001660019865-E-C03

description: Library name: Sample 266


title: S. Typhimurium treated with 0.2% MUC2. Exp 3.

city: Ithaca

first: Jeongmin

last: Song

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

description: Library name: STm_MUC2_3

data_processing:
The pooled libraries were sequenced using MinION flow cells (R9.4.1) or Flongle cells with MinKNOW v21.06.0 (ONT). Raw reads were base-called, filtered (minimum Q score > 7), debarcoded, and aligned with the S. Typhimurium LT2 genome using Guppy v5.0.11 (ONT, RRID:SCR_023196). Normalization was performed with DESeq2 (alpha = 0.01, a cutoff for read counts = 10), and data were visualized with Prism v10 (GraphPad, RRID:SCR_002798). Genes with an adjusted P value (Padj) < 0.01 and log2 fold change > 1 were considered statistically significant.
Supplementary files format and content: fastq

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium

extract_protocol:
S. Typhimurium were cultured in LB.3 supplemented with or without 0.2% purified porcine MUC2 for 3 hours at 37 °C. After fixing the cells in 100% cold methanol for 1 hour at -20 °C, the pellet was washed with RNAprotect Bacteria Reagent (Qiagen, cat. #76506), followed by lysis in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) containing lysozyme (1 mg/ml). RNA extraction was performed using the Qiagen RNeasy Mini Kit (Qiagen, cat. #74104) with in-column DNase digestion (Qiagen, cat. #79254). The RNA concentration was measured using the Qubit RNA HS kit (Invitrogen, cat. # Q32852), and RNA quality was assessed by agarose gel electrophoresis.
4 µg of total RNA was hybridized with in-house oligomer mixes specific to S. Typhi rRNA (71 oligomers, 7 µM each, Table S4) and digested with thermostable RNase H (NEB, cat # M0523S) for 30 min at 60 °C, followed by DNase I digestion (DNase I-XT, NEB, cat # M0570S) for 30 min at 37 °C. Note that in-house oligomers were designed by using the Oligo-ASST program (Phelps et al., 2021). cDNA libraries were prepared using the Maxima H Minus Double-Stranded cDNA Synthesis Kit (ThermoFisher, cat # K2561) with random hexamers. The purified libraries were end-prepped with the Ultra II End-prep mix (NEB, cat # E7546L), barcoded (ONT, cat # EXP-NBD104687), and pooled for adaptor ligation (ONT, cat # EXP-NBD104). RNAclean XP beads (Beckman Coulter, cat # A63987) and AMPure XP beads (Beckman Coulter, cat # A63880) were used for RNA and DNA purification, respectively, at each required step.

value: S. Typhimurium


title: Mice, WT, ZT9

description: Library name: Mice_WT_ZT9


title: DSP-1001660019865-E-C02

description: Library name: Sample 265


title: HepG2_FFA_9CisRA

city: Taichung City

first: Tsai

last: Shih-Chang

address: No. 100, Sec. 1, Jingmao Rd, Beitun Dist

department: Department of Biological Science and Technology

country: Taiwan

institute: China Medical University

description: Library name: Sample 2

data_processing:
Clean reads were aligned to the human reference genome (GRCh38), and gene-level read counts were generated. Differential expression analysis was performed using DESeq2 with an adjusted p-value < 0.05 and |log2 fold change| > 1.
Assembly: Human reference genome GRCh38
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts generated from RNA-seq data. Rows represent genes and columns contain read count values for each sample.

source_name: liver

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin–streptomycin at 37 °C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and integrity was assessed with an Agilent Bioanalyzer 2100.
Poly(A)+ mRNA was enriched from total RNA using oligo(dT)-coupled magnetic beads. RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: To establish an in vitro steatosis model, free fatty acids (FFAs) consisting of oleic acid and palmitic acid (2:1 molar ratio) were conjugated with bovine serum albumin (BSA) and applied at a final concentration of 1 mM for 24 h. For RXRα activation studies, FFA-treated cells were incubated with 9-cis-retinoic acid (9-cis-RA; Sigma-Aldrich, St. Louis, MO, USA) at concentrations of 1, 5, or 10 μM for 24 h.

value: liver

value: hepatocellular carcinoma cell line

value: 1 mM FFA + 10 μM 9-cis-retinoic acid

value: Batch 1


title: S. Typhimurium treated with 0.2% MUC2. Exp 2.

description: Library name: STm_MUC2_2


title: HepG2_FFA

description: Library name: Sample 1

value: 1 mM FFA


title: Mice, WT, ZT3

description: Library name: Mice_WT_ZT3


title: DSP-1001660019865-E-C01

description: Library name: Sample 264


title: S. Typhimurium treated with 0.2% MUC2. Exp 1.

description: Library name: STm_MUC2_1


title: VCaP cells, si CDO1C biol rep  3

city: Créteil

first: Virginie

last: Firlej

address: Ur Trepca

institute: UPEC TrePca

description: Library name: siCDO1C_3

data_processing:
Raw image files were converted to base‑called reads using Illumina’s CASAVA pipeline, generating FASTQ files containing read sequences and associated base‑quality scores.
Raw reads were processed using in‑house scripts to remove adapter contamination, poly‑N sequences and low‑quality reads, yielding high‑quality clean reads; standard quality metrics (Q20, Q30, GC content) were computed
Assembly: The human reference genome (hg38) and corresponding gene model annotation files were obtained from the appropriate genome repository, and a reference index was generated using HISAT2 v2.0.5. Paired‑end clean reads were aligned to hg38 using HISAT2, selected for its splice‑aware architecture and improved junction mapping accuracy.
Supplementary files format and content: xls file includes raw count for each sample

source_name: VCaP

growth_protocol: VCaP cell line was obtained from ATCC (ATCC-CRL-2876, Manassas, VA). Cells were cultured in DMEM medium (Thermofischer) supplemented with 10% fetal bovine serum, 50 IU/mL penicillin, 100 µg/mL streptomycin and 2 nM DHT. All cells were cultivated at 37°C, 5 % CO2 under humidified atmosphere

extract_protocol:
RNA were harvested using miniRNeasy kit (Qiagen).
RNA library were performed by novogene : ). Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads, fragmented, and converted into first strand cDNA using random hexamer primers, followed by second strand synthesis incorporating dUTP to generate strand specific (directional) libraries. Libraries underwent end repair, A tailing, adapter ligation, size selection, amplification and purification, and were assessed by Qubit and real time PCR for quantification, together with electrophoretic evaluation of fragment size distribution

value: VCaP

value: prostate cancer cells

value: CDO1 knockdown


title: OBs, APP-3

city: Cleveland

first: Wen-Cheng

last: Xiong

address: 2210 circle drive

institute: Case western reserve university

description: Library name: APP_L4

data_processing:
CLC Genomics Workbench
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Skull bone

growth_protocol: Calvariae from TgAPPswemOCN-Cre;Ai9 mice and control (mOCN-Cre;Ai9) mice were transferred to a dish containing PBS, and the soft tissues were carefully removed using tweezers. The cleaned bones were then cut into small fragments of approximately 1–2 mm² and sequentially digested with collagenase solution (37 °C, 30 min, twice) and trypsin solution (37 °C, 30 min) to remove residual soft tissue and adherent cells. After an additional collagenase digestion, the bone fragments were washed three times with culture medium and transferred to 60 mm culture dishes containing DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, 10 mmol/L β-glycerophosphate, and 50 μmol/L L-ascorbic acid-2-phosphate. The culture medium was replaced three times per week. Osteoblasts began to migrate from the bone chips after 3–5 days. After two weeks, the monolayer cells were detached by incubation with trypsin solution and replated onto 100 mm tissue culture dishes in α-MEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted from purified Td⁺ osteoblasts isolated by flow cytometry from mOCN-Cre; Ai9 and TgAPPswemOCN-Cre; Ai9 mice.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactrue's protocols

value: Skull bone

value: Osteoblast

value: TgAPPswemOCN-Cre; Ai9


title: DSP-1001660019865-E-B12

description: Library name: Sample 263

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: VCaP cells, si CDO1C biol rep  2

description: Library name: siCDO1C_2


title: S. Typhimurium untreated. Exp 3.

description: Library name: STm_untreated_3

value: untreated


title: OBs, APP-2

description: Library name: APP_L3


title: DSP-1001660019865-E-B11

description: Library name: Sample 262

value: Desmin


title: VCaP cells, si CDO1C biol rep  1

description: Library name: siCDO1C_1


title: S. Typhimurium untreated. Exp 2.

description: Library name: STm_untreated_2

value: WT


title: OBs, APP-1

description: Library name: APP-L


title: DSP-1001660019865-E-B10

description: Library name: Sample 261

value: CF


title: VcaP cells, siCDO1A biol rep  3

description: Library name: siCDO1A_3


title: S. Typhimurium untreated. Exp 1.

description: Library name: STm_untreated_1

value: S. Typhimurium


title: OBs, Ctrl-3

description: Library name: Ctrl_L3

value: mOCN-Cre; Ai9


title: VcaP cells, siCDO1A biol rep  2

description: Library name: siCDO1A_2


title: DSP-1001660019865-E-B09

description: Library name: Sample 260


title: H5/IVAX-1-31-d28


title: OBs, Ctrl-2

description: Library name: Ctrl-S


title: DSP-1001660019865-E-B08

description: Library name: Sample 259


title: H5/PBS-25-d28


title: VcaP cells, siCDO1A biol rep  1

description: Library name: siCDO1A_1


title: OBs, Ctrl-1

description: Library name: Ctrl-L


title: DSP-1001660019865-E-B07

description: Library name: Sample 258


title: VCaP cells, si Ctrl biol rep 3

description: Library name: siCTRL_3


title: H5/PBS-24-d28


title: mmp9_4

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Assembly: Species: Mus_musculus; Source: NCBI；Reference Genome Version: GCF_000001635.27_GRCm39
Supplementary files format and content: read count, FPKM, TPM

source_name: MMP9,cheek skin,mouse No. 4

growth_protocol: Healthy C57BL/6 mice (6-8 weeks) were selected and bred in Specific pathogen-free (SPF) animal chambers in separate cages. The room temperature was maintained at 20-27℃ and the normal day and night alternated, during which the normal diet was guaranteed.

extract_protocol:
After the completion of the experiment, the cheek tissue samples of mice were collected for RNA extraction and sent to Wuhan Huada BGI Sequencing Company for sequencing.
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 DNBSeq platform (BGI-Wuhan, China).

treatment_protocol: Three days before the experiment, the cheek hair of the mice were shaved until the skin was completely exposed. The mice were then intradermally injected with 5 μL MMP9 ( 1 μg / cheek ) or an equal volume of vehicle on the right cheek. Four hours after injection, the cheek tissue of the mice were collected for RNA-Seq.

value: skin


title: VCaP cells, si Ctrl biol rep 1

description: Library name: siCTRL_1


title: DSP-1001660019865-E-B05

description: Library name: Sample 256

value: IA


title: H5/PBS-22-d28


title: DSP-1001660019865-E-B06

description: Library name: Sample 257


title: mmp9_5

source_name: MMP9,cheek skin,mouse No. 5


title: mmp9_3

source_name: MMP9,cheek skin,mouse No. 3


title: H5/PBS-21-d28


title: DSP-1001660019865-E-B04

description: Library name: Sample 255


title: mmp9_2

source_name: MMP9,cheek skin,mouse No. 2


title: VCaP cells, si Ctrl biol rep 2

description: Library name: siCTRL_2


title: H358-RMC-6236-R/tet-MUC1shRNA_DOX+ Rep3

city: Boston

first: Shinkichi

last: Takamori

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Library name: Sample 6

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using the EdgeR-based TCC package.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample

source_name: Lung

growth_protocol: H358 RMC-6236-R cells were maintained in Gibco RPMI 1640 Media containing 10% heat inactivated FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: Lung

value: Lung cancer

value: DOX


title: PBS-13-d28


title: con_4

source_name: Vehicle,cheek skin,mouse No. 4

value: vehicle


title: DSP-1001660019865-E-A12

description: Library name: Sample 251


title: H358-RMC-6236R/tet-MUC1shRNA_DOX- Rep2

description: Library name: Sample 2

value: DMSO


title: H5/PBS-23-d28

source_name: Plasma


title: H358-RMC-6236R/tet-MUC1shRNA_DOX- Rep1

description: Library name: Sample 1


title: DSP-1001660019865-E-B03

description: Library name: Sample 254


title: H358-RMC-6236-R/tet-MUC1shRNA_DOX+ Rep2

description: Library name: Sample 5


title: DSP-1001660019865-E-A10

description: Library name: Sample 249


title: H358/tet-MUC1shRNA_DOX+ Rep3

description: Library name: Sample 6

growth_protocol: H358 cells were maintained in Gibco RPMI 1640 Media containing 20% heat inactivated FBS.


title: DSP-1001660019865-E-B02

description: Library name: Sample 253


title: H358-RMC-6236R/tet-MUC1shRNA_DOX- Rep3

description: Library name: Sample 3


title: mmp9_1

source_name: MMP9,cheek skin,mouse No. 1


title: DSP-1001660019865-E-B01

description: Library name: Sample 252


title: con_3

source_name: Vehicle,cheek skin,mouse No. 3


title: H358-RMC-6236-R/tet-MUC1shRNA_DOX+ Rep1

description: Library name: Sample 4


title: PBS-11-d28


title: WT_Mock-1

city: Hong Kong

first: Shumin

last: LIANG

address: 224 Waterloo Road, Kowloon Tong, HK

department: Biology

institute: Hong Kong Baptist University

description: Library name: WT_M1

data_processing:
After sequencing, raw read were subjected to quality control and trimmed by using fastqc (v0.11.8) to get high-quality reads.
High-quality reads were mapped to the Arabidopsis genome (TAIR10) using hisat2 (v2.2.1).
Calculated the read counts of each gene with FeatureCounts (included in Subread v2.0.8 software) to generate the count matrix for expression analysis.
Assembly: TAIR10(Assembly: GCA_000001735.1)
Supplementary files format and content: format:txt; content:raw counts for each sample

organism: Arabidopsis thaliana

source_name: 5-day-old seedlings

growth_protocol: To grow seedlings on solid media, surface-sterilized seeds were placed on half-strength Murashige and Skoog (MS) Basal Salts (M524, Sigma-Aldrich) containing 1% (w/v) sucrose (15503-022, Invitrogen) and 1% agar (A1296, Sigma-Aldrich), with a pH of 5.8 adjusted by 1 M KOH.The plates with seeds were stratified in the dark at 4 ºC for three days and then placed in a growth chamber (Percival Scientific) at 22 ºC with 60% humidity and a light intensity of 125 mol m-2 sec-1 under a 16-h light/8-h dark photoperiod for 5 days.

extract_protocol:
Total RNA were extracted using TRIzol reagent (15596026, ThermoFisher) following the manufacturer's instruction.
The mRNA libraries (poly A enrichment) were prepared by Novogene Incorporation (Beijing, China) using reagents for Illumina.

treatment_protocol: The 5-day-old seedlings in plates were then transferred to MS liquid medium with or without 50 μM ABA (962169,Sigma-Aldrich) for 3 hours, and then sampling with liquid nitrogen.

value: 5-day-old seedlings

value: Mock


title: KMS34_Dup2_Day0

first: Bo

last: Hu

address: 10300 Campus Point Dr

institute: Bristol Myers Squibb

description: Library name: KMS34_Dup2_Day0_ATACseq

library_source: genomic

data_processing:
Paired-end FASTQ files were adapter trimmed and quality filtered using fastp with automatic detection of paired-end adapters
Trimmed reads were aligned to the human reference genome hg38 using bwa-mem2 in paired-end mode.
Aligned reads were collated by read name using samtools collate to prepare the BAM file for duplicate marking.
PCR/optical duplicate reads were marked using Picard MarkDuplicates.
Duplicate-marked BAM files were coordinate sorted using samtools sort and indexed using samtools index.
Reads were filtered using samtools view to retain only properly paired, uniquely mapped primary alignments with mapping quality ≥ 30, while excluding unmapped reads, secondary alignments, duplicate reads, and supplementary alignments. Only reads mapping to included reference chromosomes were retained
Peaks were called from the filtered paired-end BAM files using MACS3 callpeak with BAMPE input format, human genome size (hs), and q-value cutoff 0.01
Genome-wide coverage tracks were generated from filtered BAM files using deepTools bamCoverage, with read centering, blacklist exclusion, and CPM normalization, producing bigWig files
Assembly: hg38
Supplementary files format and content: narrrowPeak
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: Cell lines were maintained in standard mammalian aseptic cell culture conditions at 37 °C and 5% CO2. All cell lines used in this study were cultured in RPMI 1640 supplemented with 10% heat-inactivated Fetal Bovine Serum (Gibco) and 10U/ml penicillin, 10ug/mL streptamycin

extract_protocol:
200K cells were used to perform ATAC-Seq. The cells were washed twice with 200 μL of cold PBS and spun at 600 g for 3 mins at 4 °C. Cells were then incubated with 100 μL of transposition reaction mix (50 μL 2x TD buffer, 5 μL Tn5 transposase, 44 μL Nuclease free H2O, 1 μL 10% Tween-20, 1 μL 1% Digitonin) (20034198, Illumina) and incubated on a thermomixer at 37°C for 30 mins at 750 rpm. Samples were then purified using the MinElute PCR Purification kit (28004, Qiagen) and stored at -20°C.
The Nextera Index kit (FC-121-1011, Ilumina) was used for library preparation following manufactures instructions. 50 µl of reaction mix (10 μL of transposed DNA, 9.7 μL H2O, 2.5 μL Nextera i7 primer, 2.5 μL Nextera i5 primer, 0.3 μL 100x SYBR Green, and 25 μL NEBNext High-Fidelity 2x PCR master mix) was added to each sample and 5 μL was removed to perform qPCR to determine CtD (72 °C for 5mins, 98 °C for 30 secs, (98 °C for 10 sec, 63 °C for 30 sec, 72 °C for 1 min). The samples were purified using Ampure XP beads (A63881, Beckman Coulter) eluted in 20 μL TE buffer and quantified using Qubit™ DNA HS Assay Kit (Q33230, ThermoFisher) and TapeStation High Sensitivity DNA ScreenTape (5067-5584, Agilent) prior to sequencing.

treatment_protocol: Drug treatments or DMSO vehicle were administered to exponentially growing cells in fresh media at indicated concentrations. Cells were washed and diluted in fresh media containing compounds every 3-4 days over which the number of doublings were calculated from cell counts measured using Vi-CELL XR (Beckmann Coulter, CA).

value: Bone marrow

value: Multiple myeloma

tag: time point


title: KMS34_DMSO_Dup1_Day4

description: Library name: KMS34_DMSO_Dup1_Day4_ATACseq


title: bulk RNA-seq of human E7-TCR-T cells vaccinated with control rep_3

first: wang

last: wanting

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: E7_nc_3

data_processing:
Raw sequencing data in FASTQ format were processed using fastp to remove adapters and low-quality reads. The clean paired-end reads were aligned to the reference genome using HISAT2 (version 2.2.1). The read numbers mapped to each gene were quantified using featureCounts (version 2.0.6), and FPKM values were calculated to estimate gene expression levels. Differential expression analysis between groups was performed using the DESeq2 R package (version 1.42.0). The significance threshold was set at padj <= 0.05 and |log2(foldchange)| >= 1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing raw read counts per gene

source_name: T cell

extract_protocol:
After in vitro stimulation, primary T cells were collected and washed. Total RNA was extracted using TRIzol reagent according to the manufacturer's protocol. The RNA quality and concentration were assessed before library preparation.
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 second-strand cDNA synthesis. The sequencing library was constructed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was checked with Qubit, real-time PCR, and a bioanalyzer.

value: T cell

value: E7-TCR-T cells

value: vaccinated with control


title: H5/ALC/CpG-95-d14

first: Li

last: Liang

address: 847 Health Sciences

institute: University of California Irvine

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.


title: H5/ALC/CpG+MPLA-101-d14


title: H358/tet-MUC1shRNA_DOX+ Rep2

description: Library name: Sample 5


title: H358/tet-MUC1shRNA_DOX+ Rep1

description: Library name: Sample 4


title: H5/ALC/CpG-93-d14


title: H358/tet-MUC1shRNA_DOX- Rep2

description: Library name: Sample 2


title: DSP-1001660019865-E-A11

city: Dallas

first: Chengsong

last: Zhu

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: Sample 250

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw read counts in DCC
Supplementary files format and content: RNA_Q3_normalied_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: H5/ALC/CpG+MPLA-103-d14

city: Irvine


title: con_2

source_name: Vehicle,cheek skin,mouse No. 2


title: H5/ALC/CpG+MPLA-102-d14


title: BMDM, BCG, Mtb, 6h 1

city: Shanghai, China

first: Cheng

last: Peng

state: Shanghai (31)

address: Zhengmin Road

institute: Tongji University

description:
Library name: BG_1
BCG-1

data_processing:
The raw data was handled bySkewer and data quality was checked by FastOC vO.11.2(http://www.bioinformatics.babraham.ac.uk/projects/fastgc/ ). The read length was2x150 bp. Clean reads were aligned to the Human genome hg38 using STAR.StringTie.
The expression of the transcript was calculated by FPKM (Fragments PerKilobase of exon model per Million mapped reads) using Perl.
Assembly: hg38 (clarification requested)
Supplementary files format and content: processed gene expression matrix

source_name: BMDM

extract_protocol:
Total RNA was isolated from each thymic sample using the RNAmini kit ( Qiagen,Germany). RNA quality was examined by gel electrophoresis and with Qubit(Thermo, Waltham, MA, USA).
Strand-specific libraries were constructed using the TruSeg RNAsample preparation kit (llumina, San Diego, CA, USA), and sequencing was carriedout using the lllumina Novaseg 6000 instrument.

value: BMDM

value: Bone marrow derived macrophages

value: WT

value: BCG, Mtb, 6h


title: con_5

source_name: Vehicle,cheek skin,mouse No. 5

value: skin


title: BMDM, BCGΔpe18, Mtb, 6h 2

description:
Library name: PE_2
BCGΔpe18-2

value: BCGΔpe18, Mtb, 6h


title: H5/ALC/CpG-92-d14


title: DSP-1001660019865-E-A07

description: Library name: Sample 246

value: IA


title: DSP-1001660019865-E-A06

description: Library name: Sample 245


title: PBS-12-d28


title: H358/tet-MUC1shRNA_DOX- Rep3

description: Library name: Sample 3

value: Lung

value: Lung cancer


title: BMDM, BCG, Mtb, 6h 2

description:
Library name: BG_2
BCG-2


title: BMDM, BCGΔpe18, Mtb, 6h 1

description:
Library name: PE_1
BCGΔpe18-1


title: DSP-1001660019865-E-A09

description: Library name: Sample 248


title: con_1

source_name: Vehicle,cheek skin,mouse No. 1

value: vehicle


title: DSP-1001660019865-E-A08

description: Library name: Sample 247


title: H5/ALC/CpG+MPLA-105-d14


title: ChIP_2D-iMac_day12_K27me3_Rep1

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

data_processing:
For RNA-seq, reads were trimmed using TrimGalore software (version 0.4.4) with default settings. Subsequently, the adaptor-trimmed paired-end RNA-Seq reads were aligned to the hg38 whole genome employing hisat2 with the -p16 parameter. Read counts were determined by utilizing htseq-count (version 0.11.1) and specifying the following parameters: -r pos -a 10 -t exon -s no -i gene_id -m union. Normalization of raw data counts and identification of differentially expressed genes were carried out with the aid of DESeq2 software, adhering to specific criteria (|log2fc| ≥ 1 and false discovery rate [FDR] ≤ 0.05). For ATAC-seq, all paired-end raw reads underwent processing with TrimGalore (version 0.4.4) to eliminate adapters and low-quality sequences. The adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq data were then aligned to the hg38 genome using bowtie2 (version 2.3.5) 52, employing the following parameters: --t --q --N 1 --L 25. PCR duplicates and multiply mapped reads were subsequently removed by utilizing Picard tools MarkDuplicates (available at https://broadinstitute.github.io/picard/). Following this, replicate BAM files for each time point were consolidated, and reads aligning to blacklisted genomic regions were discarded prior to peak calling with MACS253 (version 2.2.6). The enriched transcription factor motifs were analyzed using Homer (version 4.10.4, findMotifsGenome). Additionally, signal tracks for each sample were created with the bamCoverage function from deeptools and normalized to Reads Per Kilobase Million (RPKM) for ease of visualization.
Assembly: GRCh38
Supplementary files format and content: For single-cell datasets, processed data are UMI matrix and cell barcodes produced by Cellranger pipeline.
Supplementary files format and content: bw

extract_protocol:
Total RNA were extracted by TRIZol.
RNA-seq library were prepared according to SMART-seq2 protocol. ATAC-seq library were prepared according to the omni-ATAC-seq protocol.  CHIP-seq library were prepared according an ultra-low-input native ChIP-seq protocol.Single-cell libraries were prepared according to 10X genomics' manual.

value: macrophage

tag: protocol

tag: antibody


title: H358/tet-MUC1shRNA_DOX- Rep1

description: Library name: Sample 1

tag: tissue

value: DMSO


title: H5/ALC/CpG-91-d14


title: Pdgfrβ+ cells from kidney outer medulla 2 days post-IRI

city: New Haven

first: Bhavya

last: Bharathan

state: CT

address: 300 Cedar Street

department: Nephrology

institute: Yale University School of Medicine

description: Library name: PDt_MMT_S1 -Pdgfrβ MACS SORTED

data_processing:
Cell Ranger pipeline (v8.0.1) was used to process the data.
Assembly: mm10
Supplementary files format and content: Csv file, average expression of each gene grouped by clusters

molecule: cytoplasmic RNA

source_name: Kidney

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
Library was constructed following the ChromiumGEM-X_SingleCell3_ReagentKits_v4 protocol

value: Kidney


title: Mouse ovary spatial transcriptomics

type: RNA

city: Nanjing

first: Ziwei

address: Xianlin street

institute: Nanjing University of Chinese Medicine

hyb_protocol: Xenium Prime 5K Mouse Pan Tissue and Pathways Panel was used according to the manufacturer's instructions.

scan_protocol: Spatial transcriptomics was performed using the fully automated Xenium Analyzer (PN-1000529, 10x Genomics) over approximately 90 hours.

data_processing: Xenium Onboard Analysis (10x Genomics). Downstream analysis performed in R using Seurat v5.

label: Xenium probe set

source_name: ovary

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE ovary tissue blocks were sectioned at 5 µm and adhered to Xenium slides (PN-3000941, 10x Genomics). Sections were deparaffinized, decrosslinked, and processed per the Xenium FFPE tissue preparation protocol.

value: ovary

tag: tissue preservation method

value: FFPE


title: hPDL-MSCs, miR181c overexpression

city: Tokyo

first: ANHAO

last: LIU

state: Tokyo

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Periodontology

institute: Tokyo Medical and Dental University

description: Library name: miR181_RNAseq

data_processing:
Low-quality and adaptor sequences were trimmed with fastp (v0.22.0), and the processed paired-end reads were aligned to the human reference genome (GRCh38.p14) using HISAT2 (v2.1.0). Transcript assembly and abundance estimation were conducted using StringTie (v2.1.1).
Differential expression analysis was performed in R using edgeR (v4.0.16) and limma (v3.58.1; voom v1.32.0), applying thresholds of adjusted P < 0.01, FDR < 0.1, and fold change ≥ 1. P values were adjusted for multiple testing using the Benjamini-Hochberg method and converted to q values.
Assembly: GRCh38.p14/Homo_sapiens.GRCh38.112
Supplementary files format and content: CSV files contains count data.

source_name: mesenchymal stem cell

growth_protocol: We used alpha-minimum essential medium (⍺-MEM; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific), 100 U ml−1 penicillin and 100 μg ml−1 streptomycin (P/S; Thermo Fisher Scientific) as the basic medium for hPDL-MSCs, and we changed the medium twice a week. Cell passaging was performed using 0.25% trypsin-EDTA (Thermo Fisher Scientific) to detach the cells.

extract_protocol:
Total RNA was harvested using QIA shredder and RNeasy mini kit (Qiagen, 74104) according to the manufacturer's protocol.
Libraries preparation was achieved through poly(A) enrichment of mRNA and sequenced on the NovaSeqX Plus system (Illumina, San Diego, US) using 150 bp paired-end reads.

treatment_protocol: Cells were treated with miRNA mimic or negative control for 24 hrs via Lipofectamine RNAiMAX (Invitrogen, 13778030). For RIP samples, RNA immunoprecipitation was conducted according to the manufacturer’s protocol of RiboCluster Profile RIP-Assay Kit. We performed  (RIP) using anti-AGO2 antibody (MBL, RN003M). Samples were collected from cells overexpressing either Negative Control mimic or mimic.

value: mesenchymal stem cell

tag: treatment

value: hsa-miR-181c-5p mimic transfection and performed RNA immunoprecipitation


title: E14 TKO AEBP2 short rescue RNA Day0 rep2

city: Seoul

first: Yingying

last: Li

state: Seoul

address: 103 Daehak-ro

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

description: Library name: E14_TKO_AEBP2_Short_rescue_Day0_RNA_rep2

data_processing:
CUTnTag: Adaptor sequences were trimmed using Cutadapt, and the filtered reads were aligned to the mouse reference genome (mm10) with Bowtie2 using default parameters. Duplicate reads were identified and removed with Samtools markdup. Reads that failed to align to the mouse genome were subsequently mapped to the Drosophila genome (dm6), and the number of Drosophila-mapped reads was used to calculate the spike-in normalization factor.  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Adapter sequences were trimmed using Trimmomatic and reads were aligned to the hg38 reference genome using HISAT2. Transcript assembly was performed with StringTie for downstream analysis. Differential gene expression analysis was carried out using DESeq2 with p-value < 0.05 and log2 |fold change| > 1.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics, 1x MEM non-Essential Amino Acids, 10mM 2-Mercaptoethanol, Leukemia inhibitory Factor, 1mM MEK1/2 inhibitor (PD0325901), 3mM GSK3 inhibitor (CHIR99021). Cells were cultured at 37°C at 5% CO2.

extract_protocol:
CUTnTag: CUT&Tag was carried out following the Epicypher protocol.  ChIP-seq: 3 x 106 cells were harvested and fixed sequentially with 2mM disuccinimidyl glutarate (DSG; Thermo Fisher, 20593) for 35 minutes followed by 1% formaldehyde for 10 minutes at room temperature. Crosslinking was quenched with 0.125M glycine, and nuclei were isolated in NE buffer and extracted nuclei were then resuspended 1% SDS lysis buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS) and sonicated by Covaris S220 sonicator (Power 175 W, Duty 10%, 200 cycles per burst) for 430 seconds to generate DNA fragments of approximately 200bp. Sheared chromatin was diluted in ChIP dilution buffer (16.7 mM Tris-HCl, pH 8.0, 0.01% SDS, 1.1% Triton X-100, 16.7 mM NaCl, 1.2 mM EDTA) and clarified by centrifugation at 13,000 rpm for 15 minutes at 4 °C. Chromatin was incubated overnight at 4 °C with Dynabeads protein A pre-bound to 2.4mg target antibody. 1 µg of Drosophila chromatin (Active Motif, #53083) and 0.1 µg of anti-Drosophila H2A.X antibody (Active Motif, #61686) were added per reaction to perform spike-in normalization. The next day, Dynabeads were washed three times with buffer A (140mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8), twice with buffer B (300mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 1% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, 10mM Tris-HCl pH 8) and once with buffer C (250 mM LiCl, 10mM Tris-HCl pH 8, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate). RNA was removed by treatment with RNAse A at 37 °C for 30 minutes and crosslinks were reversed overnight at 65 °C in the presence of Proteinase K and SDS treatment. Eluted DNAs were size selected using SPRIselect beads (Beckman B23319).  RNA-seq: cells were resuspended in 1 ml of Trizol (ThermoFisher, 15596026) and incubated for 5 minutes at room temperature. Then, 0.2 ml of Chloroform (Sigma, C2432) was added and the solution was vortexed vigorously. The mixture was centrifuged at 13,000 rpm for 15 minutes at 4°C, and the upper phase was transferred to a fresh tube. RNA was precipitated using isopropanol (Duksan, 857) and washed with ice-cold 70% ethanol (Sigma, E7023). The precipitated RNA was dissolved in DEPC-treated water (Invitrogen, AM9915G).
CUTnTag: The eluted DNA was amplified using 2x PCR master mix (Epicypher, 15-1018) with i5 and barcoded i7 primers. Subsequently, library DNA was purified with SPRIselect beads (Beckman B23319) ).  ChIP-seq: and Libraries were prepared with NEB DNA library prep kit (NEB, E7645L) following the manufacturer’s protocol. Libraries were validated using the Tapestation HS D5000 screen tape.  RNA-seq: Library preparation was performed using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit (Illumina, RS-122-2301).

value: Mouse embryonic stem cell

value: Aebp2-/- ; Mtf2-/- ; Jarid2-/- ; AEBP2-short rescue


title: NCOR2 18h Exp2 - Rep 1

city: San Francisco

first: Valerie

last: Weaver

address: 513 Parnassus Avenue, HSE 560, Box 0456

department: Department of Surgery and Center for Bioengineering and Tissue Regeneration

institute: Johns Hopkins Univeristy

description:
Library name: NCOR2_18h.exp2.NCOR2.2_22_S227_L008.markdup.q30
Draw data to be made available on SRA

data_processing:
Reads were trimmed for adapters and low-quality bases (Phred <20).
Trimmed reads were aligned to mm39 using bowtie2 (MAPQ ≥30 retained).
Duplicate-marked BAM files were generated; proper paired reads used for analysis.
Peaks were called using MACS3 (FDR ≤1%) with IgG background subtraction.
Peak counts were generated; differential analysis performed using DESeq2 (adjusted p <0.05).
Assembly: Mouse genome build mm39.
Supplementary files format and content: Processed files include deduplicated BAM files, bigWig coverage tracks, and peak count matrices.
Supplementary files format and content: Peak files (BED/narrowPeak) and differential peak analysis results with adjusted p-values and log fold changes.
Library strategy: CUT&Tag

growth_protocol: 4T07 cells (NCOR2 knockdown or EGFP control) were plated (20,000 cells/well) and grown 24–48 h before CUT&Tag.

extract_protocol:
CUT&Tag performed in situ on adherent unfixed cells using NCOR2 antibody and pA-Tn5 tagmentation.
Tagmented DNA was PCR-amplified with indexed primers, pooled, purified, and sequenced (51 bp paired-end, NovaSeq X).

treatment_protocol: Cells were treated with IFNγ (6 hr timepoint) or vehicle control.

value: Malignant neoplasms of the mouse mammary gland

value: NCOR2 Knockdown


title: ChIP_2D-iMac_day12_K4me3_Rep3


title: KMS11_NSD2LDD_Dup2_Day10

city: San Diego

description: Library name: KMS11_NSD2LDD_Dup2_Day10_ATACseq

value: Bone marrow

value: Multiple myeloma


title: DSP-1001660019865-E-D06

description: Library name: Sample 281

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: CF

tag: scan name

tag: roi

value: Desmin


title: H5/ALC-83-d14

tag: days post prime immunization


title: ChIP_2D-iMac_day12_K4me3_Rep2

tag: cell line

tag: cell type


title: H5/ALC-85-d14


title: H5/ALC-82-d14


title: ATAC_3D-iMac_day12_Rep4


title: hPDL-MSCs, Control

description: Library name: CTL_RNAseq

value: NC mimic transfection and performed RNA immunoprecipitation


title: ChIP_2D-iMac_day12_K4me3_Rep1

value: macrophage


title: hPDL-MSCs, miRLet7 overexpression

description: Library name: miRLet7_RNAseq

value: hsa-let-7c-3p mimic transfection and performed RNA immunoprecipitation


title: hPDL-MSCs, RIP_miR181c overexpression

description: Library name: miR181_RIPseq

value: hsa-miR-181c-5p mimic transfection


title: IGF2BP2/IMP2 KO MEFs transfected with IMP2-GFP, rep1

city: New York

first: Jeetayu

last: Biswas

address: 417 East 68th St

department: Molecular Pharmacology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequencing was performed by Novogene Inc., basecalling was performed using Illumina CASAVA 1.8
Sequenced reads were trimmed with cutadapt 1.12 and then aligned to the genome with STAR 020201
Alignments were processsed with samtools 1.3.1 and duplicate reads were removed using picard 2.8.2
Identification of RNA editing sites was determined using the protocol described in Rahman et al, Nature Protocols 2018 and Biswas et al, STAR Protocol 2021, publicly available at: [https://github.com/rosbashlab/HyperTRIBE/]
Assembly: hg38
Supplementary files format and content: Editing sites shared between replicates with 5% threshold provided as bedgraph files

source_name: Mouse embryo

growth_protocol: Immortalized MEFs were cultured in DMEM supplemented with penn/strep and 10% FBS

extract_protocol:
For TRIBE cells were FACS sorted directly into Trizol for RNA extraction per manufacturer protocol. NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat# E7765S) was used with at least 50ng of total RNA input for the construction of polyA selected sequencing libraries.
TRIBE RNA-seq libraries were prepared for sequencing using standard NEBNext manufacturer protocols.

value: Mouse embryo

value: MEF

value: Fibroblast

tag: genotype

value: IGF2BP2/IMP2 KO

value: GFP-IGF2BP2/IMP2 plasmid transfected


title: IGF2BP2/IMP2 KO MEFs transfected with IMP2-GFP, rep2


title: IGF2BP2/IMP2 KO MEFs transfected with IMP2-ADAR, rep2

value: IGF2BP2/IMP2-ADAR plasmid transfected


title: H5/ALC-81-d14


title: ATAC_3D-iMac_day12_Rep3


title: hPDL-MSCs, RIP_miRLet7 overexpression

description: Library name: miRLet7_RIPseq

value: mesenchymal stem cell

value: hsa-let-7c-3p mimic transfection


title: IGF2BP2/IMP2 KO MEFs transfected with IMP2-ADAR, rep1


title: H5/DOTMA/CpG+MPLA-75-d14


title: IGF2BP2/IMP2 KO MEFs transfected with mCherry-ADAR, rep2

value: mCherry-ADAR plasmid transfected


title: H5/DOTMA/CpG+MPLA-74-d14


title: hPDL-MSCs, RIP_Control

description: Library name: CTL_RIPseq

value: NC mimic transfection


title: ATAC_3D-iMac_day12_Rep2


title: IGF2BP2/IMP2 KO MEFs transfected with mCherry-ADAR, rep1


title: HUVEC_ co-cultured shGLS1_2

city: ATLANTA

first: Yong

last: Teng

state: GA

address: Bench 31 C4038, Winship Cancer Inst

institute: emory university

description:
Library name: HUVEC_GLS1_2
Cells co-cultured with exosomes derived from HN12 transfected with shGLS1

data_processing:
CASAVA  was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that could not be determined) and  low-quality reads, then mapped to hg38 whole genome using STAR (v2.5).
The counts coincide with those produced by htseq-count with default parameters. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor for each sequenced library. Differential expression analysis of two conditions was performed using the edgeR R package (v3.16.5).
Differential expression analysis between shcont and shCBS was performed using the DESeq2 R package (v2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene of each sample
Supplementary files format and content: Tab-delimited text files including FPKM values for each Sample

source_name: cell line

growth_protocol: Human HN12 cells were grown in DMEM medium containing 10% exosome-deleted FBS, 100 units/mL penicillin and 100 µg/mL streptomycin. HUVEC cells were grown in EGM®-2 Endothelial Cell Growth Medium.

extract_protocol:
Total RNA of cells was extracted with TRIzol™ reagent. NEBNext Ultra™ II RNA Library Prep Kit (Cat#NEB-E7765) was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HN12 cells were transfected with shRNA against the GLS1 gene (shCBS) and scrambled shRNA (shGFP). HUVEC were co-cultured with exosomes from HN12-shGFP and HN12-shGLS1 for 48h, respectively.

value: HUVEC

value: Human umbilical vein endothelial cells

value: Co-culture with exosome

value: same


title: H5/DOTMA/CpG+MPLA-73-d14


title: ATAC_3D-iMac_day12_Rep1

value: macrophage


title: ATAC_2D-iMac_day12_Rep4


title: H5/DOTMA/CpG+MPLA-71-d14


title: HUVEC_ co-cultured shGLS1_1

description:
Library name: HUVEC_GLS1_1
Cells co-cultured with exosomes derived from HN12 transfected with shGLS1


title: Susceptible,Panicle,normal night temperature,mock inoculated,rep 2

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Library name: S_NT_M2

data_processing:
RNA-Seq reads were first trimmed with Trim Galore version 0.6.4 (Krueger, 2019; Martin, 2011) which includes filtering reads shorter than 30 bp and low-quality ends from reads (Phred score: <20) and the option of removing reads with Ns. The quality of reads before and after trimming was confirmed using FastQC version 0.12.1 (Andrews, 2019)
The filtered reads were then aligned to the Oryza sativa Japonica genome (EnsemblPlants IRGSP-1.0; GCA_001433935.1) using STAR version 2.7.10b (Dobin et al., 2013) with default parameters and --sjdbOverhang of 149. The alignment files generated by STAR were then used to generate gene counts using Subread version 2.0.0 (featureCounts), with default parameters (Liao et al., 2014). A data matrix of gene counts for all samples was created using a custom Python script, which was used for further differential gene expression analysis
Differential gene expression analysis was performed separately for the resistant and susceptible accessions using DESeq2 version 1.38.3 (Love et al., 2014). A Wald test was employed to calculate p-values, and genes with a Benjamini-Hochberg adjusted p-value less than 0.05 and a log2 fold change greater than 1 were considered differentially expressed
Assembly: EnsemblPlants IRGSP-1.0; GCA_001433935.1
Supplementary files format and content: A tab-delimited data matrix of raw feature counts with features (genes) in rows and sample names in columns.

organism: Oryza sativa

source_name: panicle

growth_protocol: The selected accessions were grown until heading stage in the greenhouse.

extract_protocol:
Panicles were ground using 1600 MiniG® automated tissue homogenizer (Spex Sample Prep, Metuchen NJ), and total RNA was extracted using Trizol reagent (Life Technologies, Carlsbad, CA). RNA was precipitated with 5M Potassium Acetate pH 5.2, and 100% ice-cold ethanol and air-dried. RNA pellets were resuspended in 20 µl of RNAse-free water
RNA purity and integrity was evaluated using the ExperionTM Automated Electrophoresis system (BioRad, Hercules, CA).  RNA sequencing was performed by Novogene (Davis, CA) for 150 bp paired-end read sequencing on the Illumina PE250 platform

treatment_protocol: Emerging panicles were inoculated with B. glumae (Pathogen, P) or treated with water (Mock, M) and maintained at normal night temperature (22C) and high night temperature (28C) conditions for 3 days.

value: panicle

value: mock inoculation


title: H5/DOTMA/CpG-65-d14


title: Susceptible,Panicle,normal night temperature,mock inoculated,rep 3

description: Library name: S_NT_M3


title: H5/DOTMA/CpG-64-d14


title: ATAC_2D-iMac_day12_Rep3


title: HUVEC_ co-cultured shGFP_2

description:
Library name: HUVEC_GFP_2
Cells co-cultured with exosomes derived from HN12 transfected with scrambled shRNA

value: shGFP


title: Susceptible,Panicle,normal night temperature,mock inoculated,rep 1

description: Library name: S_NT_M1


title: Susceptible,Panicle,high night temperature,mock inoculated,rep 3

description: Library name: S_HT_M3


title: ATAC_2D-iMac_day12_Rep1


title: ATAC_2D-iMac_day12_Rep2


title: HUVEC_co-cultured shGFP_1

description:
Library name: HUVEC_GFP_1
Cells co-cultured with exosomes derived from HN12 transfected with scrambled shRNA


title: H5/DOTMA/CpG-63-d14


title: H5/DOTMA/CpG-62-d14


title: 3D PMS iMac at day 12

description: 10X Genomics

value: day 12


title: HCC827 cells, Osimertinib-resistant, NR2F2 (CUT&Tag)

city: Guangzhou

first: aochu

last: liu

state: Guangdong

address: No. 1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

description: Library name: Sample14

data_processing:
Raw reads were first mapped to the hg19 reference genome using Bwa (version 0.7.17) with default parameters. High-quality mapped reads were then extracted and sorted using SAMtools (version 1.13) . PCR duplicates were removed with the Picard MarkDuplicates tool (version 1.136), and blacklist regions were filtered out using bedtools (version 2.30.0).
Peaks were identified with MACS2 using default options, and Bigwig files were generated using the deepTools bamCoverage function with standard settings.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: The HCC827AR (resistance) cell lines were cultured in RPMI-1640 media, containing 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Cut&Tag was performed according to the manufacturer's instructions (TD903, Vazyme ).
The TruePrep Index Kit V2 for IIIumina (TD202, Vazyme) was used to create a library.

treatment_protocol: Osimertinib resistant cell lines, defined as HCC827AR, are estabolised by stepwise incubate the parental cell line HCC827 with increasing doses of AZD9291,from 10 nM to 500 nM. To maintained the resistance, 500 nM AZD9291 routinely supplemented in the culture medium.

value: WT

tag: chip antibody


title: Susceptible,Panicle,high night temperature,mock inoculated,rep 2

description: Library name: S_HT_M2


title: Susceptible,Panicle,high night temperature,mock inoculated,rep 1

description: Library name: S_HT_M1


title: HCC827 cells, Osimertinib-resistant, H3K4me3 (CUT&Tag)

description: Library name: Sample13


title: H5/DOTMA/CpG-61-d14


title: Resistant,Panicle,normal night temperature,mock inoculated,rep 3

description: Library name: R_NT_M3


title: HCC827 cells, Osimertinib-resistant, H3K4me1 (CUT&Tag)

description: Library name: Sample12


title: 3D PMS iMac at day 7

description: 10X Genomics

value: day 7


title: S2: Symptomatic COVID-19 sample 2 scRNAseq

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: WI

address: 8727 W Watertown Plank Road

institute: Versiti Blood Research Institute

data_processing:
Raw Illumina sequencing data was demultiplexed and fastq files were generated using 10X Genomics Cellranger mkfastq v3.0.2
Fastq files were aligned to the GRCh38 genome and unique UMI sums per gene were calculated using 10X Genomics Cellranger count v3.0.2
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: The three files per sample are 10X cellranger count output from non-empty droplets.  Valid cell barcodes and analyzed genes are present as tab-delimited files.  Unique UMI sums per gene per cell are recorded in market exchange format.

source_name: Blood Draw

extract_protocol:
PBMCs were isolated from blood draws using Lymphoprep reagent using manufacturer instructions
For the single cell drop-seq RNA expression profiling, GEM (Gel bead-in-EMulsions) generation & barcoding, post GEM-RT cleanup & cDNA

value: PBMCs

tag: infection

tag: response

value: Symptomatic


title: Resistant,Panicle,normal night temperature,mock inoculated,rep 1

description: Library name: R_NT_M1


title: HCC827 cells, Osimertinib-resistant, ID3 (CUT&Tag)

description: Library name: Sample11


title: Resistant,Panicle,normal night temperature,mock inoculated,rep 2

description: Library name: R_NT_M2


title: H5/DOTMA-53-d14

source_name: Plasma


title: Patient 10-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample10

source_name: NSCLC

value: NSCLC

value: post-treatment

value: H3K27ac (Abcam, #ab4729)


title: Patient 9-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample9


title: Resistant,Panicle,high night temperature,mock inoculated,rep 3

description: Library name: R_HT_M3


title: S1: Symptomatic COVID-19 sample 1 scRNAseq


title: A1: Asymptomatic COVID-19 sample 1 scRNAseq

value: Asymptomatic


title: Resistant,Panicle,high night temperature,mock inoculated,rep 2

description: Library name: R_HT_M2


title: Patient 7-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample7


title: C2: Healthy control 2 scRNAseq


title: Resistant,Panicle,high night temperature,mock inoculated,rep 1

description: Library name: R_HT_M1


title: H5/IVAX-1-Chol-44-d14


title: PT22_Tamoxifen_3_day_Rep2

city: Ann Arbor

first: Jeffrey

middle: A

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

description: Library name: PT22_Tamoxifen_3_day_Rep2

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2500 (125-nucleotide read length, paired end), trimmed, and aligned to the GRCm38/mm10 mouse using Bowtie2.
Assembly: GRCm38
Supplementary files format and content: bigWig files

growth_protocol: Modified PT-22 cells were cultured in DMEM supplemented with 3% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Samples were washed with PBS and nuclei were prepared using the NE-PER Nuclear and Cytoplasmic Extraction Reagents Kit (Invitrogen).
Nuclei were resuspended in 50 μl of 1× TD buffer, then incubated with 2–2.5 μl Tn5 enzyme for 30 min at 37 ⁰C (DNA Library Preparation Kit, Nextera). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB). qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter).

treatment_protocol: Cells were treated with 1 uM 4-hydroxytamoxifen 2 d to deplete PAX8 or with vehicle. Samples were collected at 0, 3, 24 d.

value: Kidney

value: Proximal tubule

value: 4-hydroxytamoxifen (1 uM)

tag: replicate


title: C1: Healthy control 1 scRNAseq


title: H5/IVAX-1-Chol-43-d14


title: Patient 6-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample6


title: Susceptible,Panicle,normal night temperature,inoculated B.glumae,rep 2

description: Library name: S_NT_P2

value: B.glumae inoculation


title: Patient 5-NSCLC, pre-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample5

value: pre-treatment


title: S2: Symptomatic COVID-19 sample 2 bulkRNAseq

data_processing:
Fastq data were aligned using STAR aligner and MAPR-Seq workflow v3.0
Genome_build: GRCh38.p13 Gencode v32 (based on Ensembl v98)
Supplementary_files_format_and_content: csv of unnormalized read counts per gene per sample

extract_protocol:
PBMCs were isolated from blood draws using Lymphoprep reagent using manufacturer instructions. RNA was isolated using Qiagen Rneasy mini kit using manufacturer's instructions
RNA-seq libraries were prepared using Illumina's TruSeq stranded mRNA library protocol with dual indexing


title: Susceptible,Panicle,normal night temperature,inoculated B.glumae,rep 1

description: Library name: S_NT_P1

value: panicle


title: H5/IVAX-1-Chol-42-d14


title: S1: Symptomatic COVID-19 sample 1 bulkRNAseq


title: Patient 4-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample4


title: Susceptible,Panicle,high night temperature,inoculated B.glumae,rep 3

description: Library name: S_HT_P3


title: H5/IVAX-1-35-d14


title: A2: Asymptomatic COVID-19 sample 2 bulkRNAseq


title: Patient 3-NSCLC, pre-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample3


title: Susceptible,Panicle,high night temperature,inoculated B.glumae,rep 2

description: Library name: S_HT_P2


title: C2: Healthy control 2 bulkRNAseq


title: H5/IVAX-1-33-d14


title: Resistant,Panicle,normal night temperature,inoculated B.glumae,rep 3

description: Library name: R_NT_P3


title: C1: Healthy control 1 bulkRNAseq


title: Patient 1-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample1


title: Cholestasis, plasma, replicate 3

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: Library name: Sample_106

data_processing:
The AmpliSeq panel targets around 20,800 human RefSeq genes with >18,300 protein-coding genes.
The read quality was assessed using the FastQC software.
The reads were mapped to the human genome (GRCh38) using the STAR software, version 2.7.11b.
Transcript abundance was measured for the genes in the panel (the list of 20,800 genes in the panel was provided by the vendor) using the featureCounts software.
Expression normalization and differential gene expression calculations were performed using the DESeq2 software.
Assembly: GRCh38
Supplementary files format and content: Excel file of raw read count values for each Sample

source_name: Plasma extracellular vesicles

extract_protocol:
Extracellular vesicles were extracted using ExoQuick reagent and gentle centrifugation. Cell free RNA was isolated using a bead based method.
Illumina Ampliseq

value: Plasma extracellular vesicles

tag: disease

value: cholestatic


title: H5/IVAX-1-31-d14

state: CA

data_processing:
Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 3 replicate spots for each antigen was used for analysis.
Spot median pixel intensity.


title: Cholestasis, plasma, replicate 2

description: Library name: Sample_105


title: Healthy, plasma, replicate 3

description: Library name: Sample_103

value: healthy


title: H5/PBS-23-d14


title: Healthy, plasma, replicate 2

description: Library name: Sample_102


title: A2: Asymptomatic COVID-19 sample 2 scRNAseq


title: PT22_Ctrl_Rep1

description: Library name: PT22_Ctrl_Rep1


title: H5/PBS-22-d14


title: Nsd1 KO2

city: 合肥

first: 曹硕

last: 曹

state: 安徽

address: 九龙路

institute: 安徽大学

description:
Library name: SAMPLE4
Nsd1_KO_Nsd1KO_FRAS202453294-1r

data_processing:
RNA Sequencing and Differentially Expressed Genes Analysis.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mm10
Supplementary files format and content: tsv file of raw counts

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: stem cell


title: Susceptible,Panicle,high night temperature,inoculated B.glumae,rep 1

description: Library name: S_HT_P1


title: H5/IVAX-1-34-d14

city: Irvine

first: Li

address: 847 Health Sciences

institute: University of California Irvine


title: Patient 2-NSCLC, post-treatment, H3K27ac (CUT&Tag)

description: Library name: Sample2


title: H5/PBS-21-d14


title: H5/PBS-25-d14


title: Nsd1 KO1

description:
Library name: SAMPLE3
Nsd1_KO_Nsd1KO_FRAS200000017-1a


title: Single-cell RNA-seq of pooled inter-species composite iPSCs, pool B

first: Alex

last: Pollen

address: 1651 4th Street RM 473

department: Neurology

institute: UCSF

description: Library name: B

data_processing:
Reads were aligned using CellRanger version 8.0.0.
Cells were assigned to composite cell line of origin using CellBouncer's demux_vcf, with variant calls produced using separately-collected WGS data from all included cell lines.
Cells were assigned to composite cell line of origin from MULTI-seq barcode counts, using demux_tags from the CellBouncer toolkit.
We discarded all cells for which MULTI-seq indicated a cell doublet, for which the demux_vcf and demux_tags identities did not agree, or for which more than 20% of all RNA comprised mitochondrial reads.
Assembly: Human/chimpanzee/bonobo inferred ancestor genome (CAT annotated): https://doi.org/10.6084/m9.figshare.30571958.v1
Supplementary files format and content: Matrix market-format filtered cell barcode list, from CellRanger
Supplementary files format and content: Matrix market-format feature list, from CellRanger
Supplementary files format and content: Matrix market-format single cell expression matrix (for filtered cells), from CellRanger
Supplementary files format and content: Map of MULTIseq well ID to composite cell line ID (input to CellBouncer's demux_tags program)

organism: Pan troglodytes

growth_protocol: Tetraploid iPSC lines were grown in V3.1 media until 80-100% confluent and dissociated wtih Accutase.

extract_protocol:
Single-cell RNA sequencing was collected by loading approximately 20,000 cells per lane and captured using the 10x Genomics Chromium X controller with version 3.1 RNA capture kits.
Library preparation was performed according to manufacturer's instructions.

value: pooled iPSC

value: wild type


title: A549_CM272

city: Pamplona

first: Francisco

last: Exposito

state: Navarra

address: Irunlarrea SN, Research Building

department: Department of Pathology, Anatomy and Physiology, School of Medicine

country: Spain

institute: University of Navarra

data_processing:
Background correction and normalization were carried out with RMA (Robust Multichip Average) algorithm and counts were normalized using edgeR and voom. Then, a filtering process was applied to eliminate probe sets with low expression intensities in any of the experimental conditions and LIMMA (Linear Models for Microarray data) for identifying differentially expressed genes.
Assembly: GRCh38 - hg38
Supplementary files format and content: A single file containing the raw counts for each one of the samples is included

source_name: Cell line

growth_protocol: Cells were grown in either RPMI-1640 (Gibco) supplemented with 10% of HyClone Serum (Thermo Scientific), 1% penicillin-streptomycin (Lonza), at 37 °C in 5% CO2 humidified atmosphere.

extract_protocol:
RNA extraction from cell lysates was performed with the NucleoSpin® RNA kit (Macherey-Nagel) and 200ng were use for generating the libraries.
Barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs).
Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo-attached to magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA ends were end-repaired and adenylated. The NEBNext adaptor was ligated, followed by uracil excision from the adaptor and PCR amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and the DNA concentration was determined with the Qubit® fluorometer (Life Technologies). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads. FastQ files for each sample were obtained using the CASAVA v1.8 software (Illumina).

treatment_protocol: Cells were treated with CM272 or Vehicle DMSO at  the IC50 concentration for each one of the cell lines.

value: Cell line

value: lung cancer cell line


title: PBS-13-d14

last: Liang


title: Resistant,Panicle,high night temperature,inoculated B.glumae,rep 3

description: Library name: R_HT_P3


title: CTRL-E_2

description:
Library name: SAMPLE6
Ezh2_KO_CTRL_FRAS202404798-1r


title: Cholestasis, plasma, replicate 1

description: Library name: Sample_104


title: A549_Ctrl

value: DMSO


title: CTRL-P_2

description:
Library name: SAMPLE2
Nsd1_KO_CTRL_FRAS202453293-1r


title: PBS-12-d14


title: Single-cell RNA-seq of pooled inter-species composite iPSCs, pool A, replicate 2

description: Library name: A2


title: PBS-11-d14


title: H358_CM272


title: Single-cell RNA-seq of pooled inter-species composite iPSCs, pool A, replicate 1

description: Library name: A1


title: H358_Ctrl