title: A549 cells, Mock, rep 6

status: Public on Aug 02 2024

city: Albany

first: Cara

middle: T

last: Pager

address: 1400 Washington Avenue

institute: University at Albany, State University of New York

data_processing:
The quality of each fastq file was checked using the FastQC program (version 0.11.9).
Each fastq file underwent adapter trimming to improve quality using the program fastp (version 0.22.0).
Trimmed fastq files were aligned to the human reference genome, hg38, using STAR (version 2.7.10a) with the --quantMode GeneCounts specified to obatin gene expression abundance files.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contain read count abundance files for each sample after adapter trimming.

growth_protocol: Human lung adenocarcinoma cells (ATCC CCL-185) were maintained in Dulbecco’s minimal essential media (Gibco) supplemented with 10% fetal bovine serum (Seradigm, Avantar), 10 mM nonessential amino acids (Gibco), 2 mM L-glutamine (Gibco) and grown at 37°C with 5% CO2.

extract_protocol:
GENEWIZ protocol of RNA extraction with TRIzol.
GENEWIZ library preparation protocol with polyA selected RNA using Illumina kit.

treatment_protocol: A549 cells were seeded a day before infection and incubated at 37oC overnight. The next day, cells were about 80% confluent, and one culture plate was trypsinized and counted to calculate the viral volume needed for a multiplicity of infection (moi) of 10. Cells were incubated with ZIKV or PBS for mock infection at 37oC for 1 hour, rocking every 15 minutes. Afterwards, 9 ml of media was added to cells and the ZIKV- and mock-infected cells were incubated at 37oC for 48 hours.

value: human lung adenocarcinoma cells

value: Mock infection

value: PBS


title: A549 cells, Mock, rep 2

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: A549 cells, Mock, rep 1


title: A549 cells, ZIKV infected, rep 1

value: ZIKV infection

value: ZIKV


title: Bulk RNA-seq RT+ TGFb_2

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

description: RNA-seq (TGFb)

data_processing:
RNA-seq: Raw reads of mRNA sequencing were first trimmed for adaptors and low-quality bases using Trimmomatic v0.36 software. Clean reads were aligned to the human reference genome (GRCh38.p12), coupled with the comprehensive gene annotation file (GENCODEv31) using STAR v2.7.1a. Gene expression was then quantified by counting unique mapped fragments to exons using featureCount function from the Subread package. Raw counts for each gene were normalized to fragments per kilobase of transcript, per million mapped reads (FPKM)-like values.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene FPKM values for each Sample
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: skin

extract_protocol:
Total RNA was extracted from fibroblasts using miRNeasy mini kit (Qiagen, Hilden, Germany) and RNA integrity was examined using the Agilent RNA 6000 Nano Kit and 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).
The RNA-seq library preparation and sequencing were performed by Illumina NovaSeq 6000 SP-300 or DNBSEQ-G400 (2x150 bp).

tag: tissue

value: skin

value: Dermal fibroblast

tag: Sex

value: Female

tag: age

value: Radiotherapy_TGFb treatment


title: A549 cells, ZIKV infected, rep 2


title: A549 cells, ZIKV infected, rep 3


title: Bulk RNA-seq RT+ TGFb_1

description: RNA-seq (TGFb)


title: Bulk RNA-seq RT+ Ctr_2

description: RNA-seq (TGFb)


title: Bulk RNA-seq RT+ Ctr_1

description: RNA-seq (TGFb)


title: 32889_7_11_CM-R⁻

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

description: Plasma derived extracellular vesicle RNA

data_processing:
RNAseq reads were quantified using Kallisto
EdgeR was used to normalize read counts for sequencing depth and gene length
Assembly: Homo Sapiens GRch38.104
Supplementary files format and content: supplementary file containing data in the units of counts per million (CPM)

source_name: Plasma

extract_protocol:
RNA was extracted using Isolate II RNA kit (Bioline) following Manufacturer’s instructions
Library preparation was performed using NEBNext Ultra II FS DNA Library Prep Kit following manufacturer’s instructions

value: Plasma

value: not applicable

tag: genotype

value: CM-R⁻


title: 32889_8_15_CM-R⁺

value: CM-R⁺


title: Bulk RNA-seq RT- TGFb_1

description: RNA-seq (TGFb)

value: Non-irradiated_TGFb treatment


title: 32889_8_14_CM-R⁺


title: Bulk RNA-seq RT- Ctr_2

description: RNA-seq (TGFb)


title: RM td TOMATO 30A SWIRLER BASE RETA DAY 3-14

status: Public on Aug 03 2024

city: Melbourne

first: Jacky

middle: Yisheng

last: Li

state: Victoria

address: 50 Flemington Rd

department: Cellular Biology

country: Australia

institute: MCRI

data_processing:
For single cell data, sequenced reads were mapped to the GrCh38 whole human genome with cell ranger software using the default parameters.
Assembly: hg38
Supplementary files format and content: Features and barcodes and count matrix for single cell data (feature.tsv, barcodes.tsv, matrix.mtx).

source_name: RM td TOMATO

growth_protocol: iPSC from two independently generated lines were differentiated in Swirling EB cultures to hematopoietic cells over a 14 day period, through sequential stages of mesoderm induction, HOXA patterning, endothelial specification, and endothelial to hematopoietic transition. After 14 days differentiation, blood cells shed into the medium (termed supernatant cells) were harvested as were cells disaggregated from the remaining swirling EB structures (termed swirler base). These samples were analysed separately.

extract_protocol:
Single cell suspensions for each sample were harvested and used for single cell droplet generation, RNA extraction and library preparation in a Chromium controller according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Selected samples were treated with the retinoic acid precursor retinyl acetate (2µM RETA) added at day 3 of differentiation for two days and removed at day 5, or replenished every two days. In these latter samples, RETA was removed at day 11, day 13 or day 14.

value: RM td TOMATO

value: IPSC induced stromal and endothelial cell

value: 30A RETA DAY 3-14


title: 32889_8_9_CM-R⁺


title: Bulk RNA-seq THBS1_OE_2

description: RNA-seq (CRISPR/dCas9)

value: CRISPR/dCas9 targeting THBS1


title: Bulk RNA-seq RT- Ctr_1

description: RNA-seq (CRISPR/dCas9)


title: Bulk RNA-seq THBS1_OE_1

description: RNA-seq (CRISPR/dCas9)


title: 32889_8_3_CM-R⁻


title: Bulk RNA-seq Ctr_2

description: RNA-seq (CRISPR/dCas9)

value: CRISPR/dCas9 empty vector


title: 32889_7_10_CM-R⁻


title: Bulk RNA-seq Ctr_1

description: RNA-seq (CRISPR/dCas9)


title: 32889_8_7_CM-R⁺


title: 32889_8_16_CM-R⁺


title: 32889_7_4_CM-R⁻


title: 32889_7_8_CM-R⁺


title: 32889_7_18_CM-R⁻


title: 32889_7_2_CM-R⁺


title: FAT_con_2

city: Dallas

first: Yinshi

last: Ren

state: Texas

address: 2222 Welborn St

institute: Scottish Rite for Children

data_processing:
cDNA are a-tailed and indexed adapters are ligated.   After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200. Before being normalized and pooled, samples  are quantified by Qubit then run on the Illumina NextSeq 2000.
Assembly: GRCm39

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Total RNA was extracted from the 24 mm inserts with PureLinkTM RNA Mini Kit (Thermo Fisher Scientific).
Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring  only high quality RNA is used (RIN Score 8 or higher).   The Qubit fluorimeter is used to determine the concentration prior to staring library prep.  One microgram of total DNAse treated RNA is then prepared with the  TruSeq Stranded mRNA Library Prep Kit from Illumina.

value: bone marrow

value: macrophage

value: WT

value: cells and necrotic fat are put in a transwell system to induce direct contact and phagocytosis


title: FAT_con_1


title: FAT_high_1


title: crRaf1_crPkm2_rep3

city: Wuhan city

first: Qian

last: Chen

state: Hubei province

address: No.299 bayi road, wuchang district

department: College of Life Sciences

country: China

institute: Wuhan University

data_processing:
The original raw data obtained from high-throughput were first subjected to trimmomatic (version 0.39) for quality control and adaptor trimming, the trimmed reads which length was short than 50bp were filtered.
Then clean date were mapped to the mouse genome (GRCm39) using STAR(version 2.7.10b) with default parameters, and transcriptome were prepared based on the Refseq annotation of mouse downloaded from the table browser of UCSC database.
Read counts were calculated with subread (version 2.0.1), and gene expression was quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) values, and gene with FPKM >0.5 were considered to be expression.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver hepatoma

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were collected by centrifugation and added to the lysate, the RNA was harvested by using MolPure® Cell/Tissue Total RNA Kit ( Cat#19221ES50, Yeasen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver hepatoma

value: hepatocarcinoma cell

value: Raf1_Pkm2 knockout

value: RNA-seq


title: 32889_8_11_CM-R⁺

value: Plasma

value: not applicable


title: crRaf1_crPkm2_rep2


title: 32889_7_19_CM-R⁺

value: CM-R⁺


title: crRaf1_crPkm2_rep1


title: 32889_7_22_CM-R⁻

value: CM-R⁻


title: Bulk RNA-seq RT- TGFb_2

description: RNA-seq (TGFb)

value: skin

value: Dermal fibroblast

value: Female

value: Non-irradiated_TGFb treatment


title: crPkm2_rep3

value: Pkm2 knockout


title: 32889_8_10_CM-R⁺


title: cSAM-control, bio rep 1

city: Tokyo

first: Yu-Hsuan

last: Chang

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to the mouse reference genome (mm10) using Rsubread (v2.4.3). Raw counts were obtained from read alignments using refGene for gene counts or RepeatMasker annotation for transposable elements, and then further transferred to CPM using edgeR (v3.32.1). After filtering out low-expression genes with CPM < 1, all CPM values were performed with log2 transformed for further analysis.
Assembly: mm10
Supplementary files format and content: csv files include CPM values for each Sample

source_name: mouse bone marrow cells transformed by SETBP1 and ASXL1 mutations

growth_protocol: Mouse cSAM cells were cultured in RPMI-1640 medium, 10% FBS (Biosera), 1 ng/ml mouse interleukin-3 (IL-3, R&D systems), and 1% penicillin-streptomycin.

extract_protocol:
Total RNA of 2 x10^6 cultured Setdb1-depleted or non-targeting control cSAM cells in each sample was extracted by RNeasy Mini Kit (QIAGEN).
rRNA depletion stranded Library. Ribosomal RNA was removed by RNase H. After RNA fragmentation, cDNA was synthesized by random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP. Following end repair, add A and adaptor ligation, the DNA fragments were amplified by PCR.

tag: strain

value: cSAM


title: 32889_8_4_CM-R⁺


title: 32889_7_20_CM-R⁻


title: crPkm2_rep2


title: crRaf1_rep3

value: Raf1 knockout


title: FAT_high_2

value: bone marrow

value: macrophage

value: WT


title: crRaf1_rep2

value: Liver hepatoma

value: hepatocarcinoma cell


title: 32889_8_5_CM-R⁻


title: WT_rep3

value: Wild type

value: RNA-seq


title: crRaf1_rep1


title: 32889_7_17_CM-R⁻

value: Plasma

value: not applicable


title: 32889_7_23_CM-R⁻

value: CM-R⁻


title: WT_rep1


title: WT_rep2


title: Lb2 cell_SOCA_Day14

library_source: genomic

data_processing:
Thecleandatawasgeneratedbytrimminglowqualitybasesatbothendsofreadandremoveshortfragments,thisworkwascompletedbysequencingcompany
For deep-seq, the data was handled by CRISPRessoPooled
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: txt files include DNA sequences for each sample

molecule: genomic DNA

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

value: Sequencing of the SOCA library


title: 32889_8_12_CM-R⁻


title: Lb2 cell_SOCA_Day12


title: Lb2 cell_SOCA_Day10


title: 32889_8_17_CM-R⁻


title: 32889_7_12_CM-R⁻


title: 32889_7_9_CM-R⁻


title: 32889_7_15_CM-R⁻


title: crPkm2_rep1


title: Lb2 cell_SOCA_Day8


title: Lb2 cell_SOCA_Day6


title: 32889_7_21_CM-R⁻


title: 32889_7_1_CM-R⁻


title: 32889_8_1_CM-R⁻


title: 32889_8_2_CM-R⁻


title: Ce cell_Parallel_Day14

value: Sequencing of the Parallel library


title: 32889_7_16_CM-R⁻


title: Lb2 cell_SOCA_Day4


title: 32889_8_13_CM-R⁻


title: 32889_7_24_CM-R⁻


title: Ce cell_Parallel_Day12


title: Ce cell_Parallel_Day10


title: DN

city: beijing

first: xiaowei

last: tang

state: beijing

address: xuyuanlu 38

institute: 北医

library_source: transcriptomic single cell

data_processing:
The Seekoul Tools pipeline was utilized to process the reads and generate the transcript expression matrix. Initially, the cell barcodes and Unique Molecular Identifier (UMI) sequences were extracted based on a defined pattern that localized the barcode, linker, and UMI within each read. The extracted barcodes were corrected using a whitelist, and the corrected barcode, along with the UMI, were placed in the header of their respective reads. Next, the reads were aligned to the reference genomes using STAR 2.5.1b. Subsequently, reads containing barcode and UMI information were assigned to the transcriptome using featureCounts from the Subread package 1.6.4, with the default parameters except for "-s 1-fracOverlap 0.5". This step resulted in a raw UMI count matrix based on barcodes and transcripts, similar to the raw_feature_bc_matrix output of Cell Ranger.
Assembly: hg38
Supplementary files format and content: Table-seprarated values files and matrix files

source_name: female breast normal tissue

extract_protocol:
Freshly collected tissue samples were immediately washed with RPMI1640 medium (Gibco, Life Technologies) and dissociated using a Multi-tissue dissociation kit 2 (Miltenyi 130-095-929). The addition of DNase was dependent on the viscosity of the homogenate. Subsequently, cell counts and viability were determined using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent, following the removal of erythrocytes (Miltenyi 130-094-183). The decision to perform debris and dead cell removal was made based on experimental requirements (Miltenyi 130-109-398/130-090-101). Finally, the freshly isolated cells were again washed twice with medium and resuspended at a concentration of 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin (BSA) (Thermo Fisher Scientific).
Single-cell RNA-Seq libraries were prepared using the SeekOne® MM Single Cell 3' library preparation kit (SeekGene Catalog No.). Briefly, an appropriate number of cells were loaded into the flow channel of the SeekOne® MM chip, which contained 170,000 microwells, and allowed to settle in the microwells by gravity. After removing unsettled cells, Cell Barcoded Magnetic Beads (CBBs) was pipetted into the flow channel and also allowed to settle in the microwells with the assistance of a magnetic field. Next, excess CBBs were removed, and the cells in the MM chip were lysed to release RNA, which was captured by the CBB in the same microwell. Subsequently, all CBBs were collected, and reverse transcription was performed at 37°C for 30 minutes to label the cDNA with the cell barcode on the beads. Exonuclease I treatment was then carried out to remove unused primers on the CBBs. Following that, the barcoded cDNA on the CBBs was hybridized with a random primer that had the 2 SeqPrimer sequence on the 5' end and could extend to form the second strand DNA with the cell barcode on the 3' end. The resulting second strand DNA was denatured off the CBBs, purified, and amplified in a PCR reaction. The amplified cDNA product was subsequently purified to remove unwanted fragments and added to full-length sequencing adapters and sample indices by indexed PCR. The indexed sequencing libraries were cleaned up with SPRI beads, quantified using quantitative PCR (KAPA Biosystems KK4824), and then sequenced on the Illumina NovaSeq 6000 platform with PE150 read length or the DNBSEQ-T7 platform with PE150 read length.

value: female breast normal tissue


title: 32889_8_8_CM-R⁻


title: 32889_8_6_CM-R⁻


title: Ce cell_Parallel_Day8


title: 32889_7_7_CM-R⁻


title: Ce cell_Parallel_Day4


title: 32889_7_3_CM-R⁻


title: Ce cell_Parallel_Day6


title: Ce cell_SOCA_Day14_rep3


title: 4915

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
Reads were aligned to the human genome GRCh38 using HISAT2.
Gene counts were calculated for GENCODE v35 using htseq-count.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Liver tissues were flash frozen and stored at minus 80. Trizol reagent were used to extract RNA from frozen liver samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: metavir


title: 4695


title: Ce cell_SOCA_Day14_rep2


title: 4500


title: Ce cell_SOCA_Day12_rep3


title: 3907

value: untreated, HCV-infected


title: Ce cell_SOCA_Day12_rep2


title: 3950


title: 3657


title: Ce cell_SOCA_Day10_rep3


title: S76778

data_processing:
Reads were aligned to a combined genome including the human genome GRCh38 and the Mus musculus genome GRCm38 using HISAT2.
Gene counts were calculated for GENCODE v35(human) and vM15 (mouse) genome annotations using htseq-count.
Reads were further processed and normalized using DESeq2.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Tab-delimited text files include DESeq2 normalized read counts

growth_protocol: Humanized liver chimeric mice were produced by splenic injection of cryopreserved human hepatocytes (BD Biosciences, San Jose, CA) into uPA/SCID mice as previously described (PMID: 26536627). All mice were kept in isolated cages and fed ad libitum on CFR1 diet (Oriental Yeast Co., Ltd, Tokyo, Japan).

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Twelve weeks after hepatocyte transplantation, mice were injected intravenously with or without 10^5 copies of genotype 1b HCV-infected serum. After serum inoculation, mouse blood samples were obtained serially, and human albumin concentrations and serum HCV RNA levels were measured.

value: HCV-infected

tag: zeitgeber time

value: uPA/SCID


title: Ce cell_SOCA_Day12_rep1


title: Ce cell_SOCA_Day10_rep1


title: Ce cell_SOCA_Day8_rep3


title: S76780


title: Ce cell_SOCA_Day8_rep2


title: S76779


title: S76788

value: untreated


title: S76786


title: S76787


title: Ce cell_SOCA_Day6_rep2


title: Ce cell_SOCA_Day6_rep1


title: S76783


title: Ce cell_SOCA_Day14_rep1


title: Ce cell_SOCA_Day4_rep2


title: S76782


title: Tumor_D18_rep6


title: S76790


title: Tumor_D18_rep5


title: S76791


title: Tumor_D18_rep4


title: S76769


title: Tumor_D18_rep3


title: Ce cell_SOCA_Day10_rep2


title: S76772


title: S76773


title: Tumor_D18_rep2


title: Ce cell_SOCA_Day4_rep1


title: Ce cell_SOCA_Day8_rep1


title: BCBL-1_Dox_minus

type: RNA

city: Kumamoto

first: Seiji

last: Okada

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: BCBL-1, Dox, negative, replicate 1

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: BCBL-1 cells were mainteined in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated with or without Dox for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Dox negative


title: S76784


title: Ce cell_SOCA_Day4_rep3


title: S76792


title: BCBL-1_Dox_plus

source_name: BCBL-1, Dox, positive, replicate 1

value: Dox positive


title: Tumor_D18_rep1


title: S76793


title: Ce cell_SOCA_Day6_rep3


title: S76789


title: S76771


title: Tumor_D10_rep5


title: S76770


title: Tumor_D10_rep4


title: S76794


title: Tumor_D10_rep6


title: Tumor_D10_rep3


title: Tumor_D10_rep2


title: S76764


title: S76795


title: SOCA library


title: S76796


title: Parallel library


title: S76765


title: S76762


title: S76763


title: S76785


title: S76797


title: S76777


title: S76776


title: S76767


title: S76768


title: B9

city: Nudapest

first: Bálint

middle: Kende

last: Szeredás

address: Korányi Sándor street 2/a

department: Department of Internal Medicine and Oncology - Department of Endocrinology

country: Hungary

institute: Semmelweis University

data_processing:
fastq.gz files were uploaded to GeneGlobe (QIAGEN) for analysis, which performed adopter trimming, discarded low-quality reads, and aligned the results to GRCh38 using bowtie. Readcounts for miRNA were achived by mapping the results to miRBase v21.
Normalization, DeSeq2 and the neural network algorithm were then ran locally, using R.
Assembly: GRCh38, MirBase v21, piRNABank
Supplementary files format and content: .xlsx microRNA raw data count

source_name: pancreatic neuroendocrine tumor, formalin-fixed paraffin-embedded

extract_protocol:
Total RNA was isolated from the macrodisected 80 μm FFPE samples using RecoverAllTM Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, Waltham, MA, U.S.)
The libraries were constructed using the QiaSeq miRNA Library Kit by QIAGEN.
5 µl-s of isolate were used for each library. After library preparation, a Qubit 4 fluorimeter was used, to measure library concentrations, and to achieve equimolar pooling, then the NebNext Library Quant Kit (New England Biolabs) was utilised to measure the final pooled concentration before sequencing

tag: grade

value: Grade 1


title: B6

value: pancreatic neuroendocrine tumor, formalin-fixed paraffin-embedded


title: B7

value: Grade 2


title: B10

value: Grade 3


title: B4


title: B11


title: B5


title: B12


title: B3


title: Tumor_D10_rep1

value: Liver hepatoma

value: hepatocarcinoma cell

value: Wild type


title: B8


title: S76774


title: S76781


title: S76775


title: B1


title: S54_H3k27ac

data_processing:
Reads were aligned to the human genome hg38 using Bowtie.
Peaks were called on down-sampled human read alignments using the macs3 peak caller.
Supplementary files format and content: Tab-delimited files containing macs3 predicted peak regions.

extract_protocol:
Frozen liver tissues were homogenized in PBS and cross-linked with formaldehyde and the reaction was stopped by the addition of glycine at room temperature. subsequently, liver tissues were lysed and chromatin was extracted and sonicated to generate 200-500 base pair fragments, which were used for immunoprecipitation.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: S77_H3k27ac


title: input3 NNK

city: Barcelona

first: Mariano

last: Martín

address: c/ Baldiri Reixac 10-12

country: Spain

institute: IBEC

description: from plasmid library

data_processing:
FastQ files from paired-end sequencing of each library library before (‘input’) and after selection (‘output’) were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Assembly: no genome used for assembling - Random Library
Supplementary files format and content: excel book (.xlsx). Processed sequencing data. Each sequence has nucleator status (1 o 0) and a mean nucleation score

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
Input and output pellets were thawed and resuspended in 1.5 ml extraction buffer (2% Triton-X, 1% SDS, 100 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA pH 8), and underwent two cycles of freezing and thawing in an ethanol-dry ice bath (10 min) and at 62˚C (10 min). Samples were then vortexed together with 1.5 ml of phenol:chloroform:isoamyl 25:24:1 and 1.5 g of glass beads (Sigma). The aqueous phase was recovered by centrifugation and mixed again with 1.5 ml phenol:chloroform:isoamyl 25:24:1. DNA precipitation was performed by adding 1:10 V of 3M NaOAc and 2.2 V of 100% cold ethanol to the aqueous phase and incubating the samples at -20°C for 1 hr. After a centrifugation step, pellets were dried overnight at RT. Pellets were resuspended in 900ul resuspension buffer (10 mM Tris pH 8, 1 mM EDTA pH 8) and treated with 7.5 ml RNase A (Thermo Scientific) for 30 min at 37˚C. The DNA was finally purified using 30ul of silica beads (QIAEX II Gel Extraction Kit, Qiagen), washed and eluted in 30 ul of elution buffer. Plasmid concentrations were measured by quantitative PCR with SYBR green (Merck) and primers annealing to the origin of replication site of the PCUP1-Sup35N plasmid at 58 °C for 40 cycles.
The library for high-throughput sequencing was prepared in a two-step PCR (Q5 high-fidelity DNA polymerase, NEB). In PCR1, 300 million of molecules were amplified for 15 cycles at 68ºC with frame-shifted primers with homology to Illumina sequencing primers (Supplementary Data Primers). The products were purified with ExoSAP treatment (Affymetrix) and by column purification (MinElute PCR Purification Kit, Qiagen). They were then amplified for 12 cycles in PCR2 with Illumina-indexed primers.
Libraries of random sequences were synthesized by Integrated DNA Technologies (IDT) as ultramers of 12 NNK codons (36 nucleotides). Sequences were flanked by constant regions of 25 nt upstream and 21 nt downstream for cloning. The NNK ultramers were extended in a 1-cycle PCR (Q5 high-fidelity DNA polymerase, NEB). The resulting products were treated with 2ul/tube of ExoSAP (ExoSAP-IT, Applied Biosystems) for 30 minutes at 37 °C and 20 minutes at 80 °C and purified through a MinElute column (Qiagen). In parallel, the PCUP1-Sup35N plasmid was linearized by PCR (Q5 high-fidelity DNA polymerase, NEB). The products were purified from a 1% agarose gel (QIAquick Gel Extraction Kit, Qiagen) and ligated by Gibson with 3 h of incubation at 50°C (Supplementary Data Table 3 Gibson) followed by dialysis for 3 h on a membrane filter (MF-Millipore 0.025 μm membrane, Merck) and vacuum concentration. The resulting libraries were transformed into 10-beta Electrocompetent E. coli (NEB), by electroporation with 2.0 kV, 200 Ω, 25 μF (BioRad GenePulser machine). Cells were recovered in SOC medium for 30 min and grown overnight in 50 ml of LB ampicillin medium. A small amount of cells was also plated in LB ampicillin plates to assess transformation efficiency. Total transformants were estimated, 50 ml of overnight culture were harvested to purify each library with a midi prep (Plasmid MIDI Kit, Qiagen).

treatment_protocol: Cells were thawed from −80 °C in 50 ml plasmid selection medium at OD = 0.05 and grown until exponential for 15 h. At this stage, cells were harvested and resuspended in 400 ml protein induction medium (-URA, 2% glucose, 100 μM Cu2SO4) at OD = 0.1. After 24 h the input pellets were collected, and cells were plated on -ADE-URA selection medium in 145-cm2 plates (Nunc, Thermo Scientific). Plates were incubated at 30 °C for 7 days. Finally, colonies were scraped off the plates with PBS 1x and harvested by centrifugation to collect the output pellets. Both input and output pellets were stored at −20 °C before DNA extraction. For each random library experiment, one input samples and three technical replicates of the output pellet were processed for sequencing.

value: yeast

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)


title: S16_H3k27ac


title: output3B NNK

description: from plasmid library


title: output3A NNK

description: from plasmid library


title: S23_H3k27ac


title: output3C NNK

description: from plasmid library


title: output2C NNK

description: from plasmid library


title: S76766


title: S44_H3k27ac


title: S73_H3k27ac


title: output2B NNK

description: from plasmid library


title: S16_Input


title: input2 NNK

description: from plasmid library


title: output1C NNK

description: from plasmid library


title: output2A NNK

description: from plasmid library


title: S98_H3k27ac


title: S93_H3k27ac


title: output1A NNK

description: from plasmid library


title: S65_H3k27ac


title: S83_H3k27ac


title: S87_H3k27ac


title: B2


title: S65_Input


title: output1B NNK

description: from plasmid library


title: GZLBM2022tissue196

type: genomic

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: Standard Illumina Protocol

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.

label: Cy3, Cy5

source_name: Brain metastasis

label_protocol: 250-500 ng of converted DNA was used as input, and labelled as per standard Illumina protocols.

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded or fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles

treatment_protocol: During sample processing, genomic DNA from each specimen was processed.

tag: disease state

value: Brain metastasis


title: S51_H3k27ac


title: GZLBM2022tissue195


title: HEK293T, DZNep Rep 4

city: Indianapolis

first: Evan

last: Cornett

state: Indiana

address: 635 Barnhill Drive

institute: Indiana University

data_processing:
Azenta Life sciences
Sequences were trimmed to remove adapter sequences and nucelotides with poor read quality using Trimmomatic v.0.36
Readers were mapped to the Homo sapiens GRCh38 reference genome using STAR v.2.5.2b
BAM files were generated using Star v.2.5.2b. Unique gene hit counts were calculated using featureCounts from Subread v.1.5.2
Read counts were normalized using deseq2
Assembly: GRCh38
Supplementary files format and content: tab deliminated file includes raw counts for each sample
Supplementary files format and content: tab deliminated file includes normalized counts for each sample

growth_protocol: HEK293T cells were grown in DMEM media supplemented with 10% Fetal Bovine Serum and antibiotics in 5% CO2 and 37 C

extract_protocol: Performed by Azenta

treatment_protocol: HEK293T cells were treated with either 100 uM DZNep (ApexBio) or vehicle control for 48 hrs.

value: human embryonic kidney

value: 100 uM DZNep


title: GZLBM2022tissue194


title: GZLBM2022tissue191


title: HEK293T, DZNep Rep 2


title: HEK293T, DZNep Rep 1


title: GZLBM2022tissue193


title: HEK293T, DZNep Rep 3


title: HEK293T, Control Replicate 3

value: Control


title: GZLBM2022tissue192


title: GZLBM2022tissue190


title: HEK293T, Control Replicate 2


title: HEK293T, Control Replicate 4


title: input1 NNK

description: from plasmid library


title: GZLBM2022tissue189


title: GZLBM2022tissue188


title: GZLBM2022tissue183


title: GZLBM2022tissue186


title: HEK293T, Control Replicate 1


title: Adult primary cortical Ecs treated with MS-257- 2 (biol rep 3)

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

data_processing:
mRNA-seq reads were quality checked using FastQC [www.bioinformatics.babraham.ac.uk/projects/fastqc/] after removing adaptors with cutadapt. .
Raw reads were mapped with STAR read aligner and default parameters against build mm10 of the mouse reference genome and the latest annotation of mouse genome from the mouse GENCODE repository
We used featureCounts to count reads on each gene for gene expression quantification.
Differentially expressed genes were detected and ranked using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary cortical endothelial cells

extract_protocol:
Direct-zol RNA MiniPrep (Zymo research R2052). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit 15μM (KK8727, Roche) following the manufacturer’s instructions.

value: Primary cortical endothelial cells

value: Cortical endothelial cells

value: WT


title: Adult primary cortical Ecs treated with MS-257- 1 (biol rep 1)


title: Adult primary cortical Ecs treated with MS-257- 2 (biol rep 2)


title: Adult primary cortical Ecs treated with MS-257- 2 (biol rep 4)


title: GZLBM2022tissue187


title: GZLBM2022tissue181


title: GZLBM2022tissue182


title: Adult primary cortical Ecs treated with Wnt3a- 1 (biol rep 1)

value: Wnt3a 200nM


title: E-13.5 cortical Ecs-3 (biol rep 3)


title: GZLBM2022tissue184


title: Adult primary cortical Ecs treated with Wnt3a-2 (biol rep 2)


title: E-13.5 cortical Ecs-2 (biol rep 2)


title: GZLBM2022tissue178


title: GZLBM2022tissue179


title: E-13.5 cortical Ecs-1 (biol rep 1)


title: Adult primary cortical Ecs control- 2 (biol rep 2)


title: GZLBM2022tissue180


title: GZLBM2022tissue177


title: Adult primary cortical Ecs control- 1 (biol rep 1)


title: GZLBM2022tissue185


title: GZLBM2022tissue174


title: GZLBM2022tissue176


title: SC15_2 - STZ_hKLF6PODTA_2 (E399)

city: Stony Brook

first: Bismark

last: Owusu Frimpong

address: 100 Nicolls Rd

institute: Stony Brook University

description: Cellbarcode/UMI: R1:28;i7 index: 8

data_processing:
Illumina software used for basecalling.
CellRanger used for raw processing
Seurat R-package used for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: A xlsx spreadsheet containing normalized expression of genes based on cluster and group

molecule: nuclear RNA

source_name: Kidney Cortex

extract_protocol:
Kidneys were perfused with HBSS and stored in RNALater at -80C. A 2 mm3 section of tissue was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2,  0.1 mM EDTA, and 0.1% TritonX-100. The tissue was initially dissociated by pipetting up and down ~10X with a p-1000 tip and then being passed through a 25G syringe ~10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) before counting by hemocytometer.  Nuclei were then diluted and prepared using the 10X Chromium System according to the manufacturer’s instructions (10X Genomics).
RNA libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

value: FVB/N

value: stz induced

tag: preparation

value: Single nuclei

tag: sample index

value: CCCTAACAATTCCGATTGGATTGCGAAGGCTG


title: Adult primary cortical Ecs control- 3 (biol rep 3)


title: GZLBM2022tissue173


title: SC15_1 - SHAM_hKLF6PODTA_2 (F354)

description: Cellbarcode/UMI: R1:28;i7 index: 8

value: sham

value: ACATTACTTTTGGGTACAGCCCACGGCAATGG


title: GZLBM2022tissue171


title: SC15_4 - STZ_NPHS2-rtTA_2 (E726)

description: Cellbarcode/UMI: R1:28;i7 index: 8

value: CATGCGATTGATATTCGTGATCGAACCCGACG


title: GZLBM2022tissue175


title: GZLBM2022tissue169


title: GZLBM2022tissue168


title: GZLBM2022tissue170


title: SMU_CoMitis_1

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

description: SMU_CoMitis_1 / Mitis_CoSMU_1

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Assembly: NC_004350.2 for S. mutans UA159; CP079724.1 for S. oralis
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: excel workbook file includes Log2 fold changes and Log10 P values from Degust output, as well as gene descriptions and normalized read counts

organism:
Streptococcus mutans
Streptococcus mitis

source_name: whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TYG medium in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential growth phase (OD600 nm ≈ 0.4)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: whole cell lysate

value: planktonic bacterial culture

value: wild-type

value: TYG; growth to OD600 nm =  0.4


title: SMU_CoMitis_2

description: SMU_CoMitis_2 / Mitis_CoSMU_2


title: P85* | 012 | TME

type: protein

city: Brisbane

first: Habib

last: Sadeghirad

state: Queensland

address: 37 Kent St, Woolloongabba, 37 Kent St, Woolloongabba

institute: The University of Queensland

hyb_protocol: DSP eluates were hybridised as per manufacturers instructions in nCounter Readout User Manual.

scan_protocol: Hybridised samples were loaded into Nanostring prep station and processed as per DSP Slide Prep User Manual. N counter was performed with default parameters, and counts from Ncounter uploaded back to DSP instrument

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

molecule: protein

source_name: HNSCC

label_protocol: DSP experiments were performed as per manufacturers DSP Slide Prep User Manual

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

value: HNSCC

tag: bestresponse

value: PD

value: TRUE

tag: pathway

value: Nivolumab

tag: mortality

value: Y

value: Male

tag: smokingstatus

value: Never

tag: pfs

value: 1 mos

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME

tag: responsesintme


title: SMU_CoMitis_3

description: SMU_CoMitis_3 / Mitis_CoSMU_3

tag: tissue

tag: strain

tag: cell type

tag: genotype

tag: treatment


title: P85* | 006 | TME

tag: age

tag: Sex


title: GZLBM2022tissue166

source_name: Lung adenocarcinoma

tag: disease state

value: Lung adenocarcinoma


title: GZLBM2022tissue165


title: P85* | 005 | TME

tag: bestresponse

tag: pathway


title: GZLBM2022tissue167

value: Brain metastasis


title: SC15_3 - SHAM_NPHS2-rtTA_2 (E409)

description: Cellbarcode/UMI: R1:28;i7 index: 8

value: FVB/N

value: sham

tag: preparation

value: Single nuclei

tag: sample index

value: CTCGTCACGATCAGCAACAACAGGTGGTGTTT


title: GZLBM2022tissue163


title: GZLBM2022tissue164


title: GZLBM2022tissue172


title: P85* | 004 | TME

tag: mortality

tag: smokingstatus

tag: pfs

tag: countofloweprgene


title: P85* | 004 | TUMOUR

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: P85* | 005 | TUMOUR

tag: tissue


title: GZLBM2022tissue159


title: GZLBM2022tissue156


title: GZLBM2022tissue162


title: GZLBM2022tissue161


title: P85* | 001 | TME


title: GZLBM2022tissue154


title: P85* | 011 | TUMOUR


title: Epimedium pubescens leaves,HN,48d,rep C

city: 北京

first: 尚年

last: 刘

state: 北京

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

data_processing:
Raw data in FASTQ format (raw reads) is processed using FASTP software and low-quality reads are filtered.
Align the obtained clean data to the reference genome using HISAT2 v2.0.5.
StringTie (1.3.3b) was used for new gene prediction.
featureCounts (1.5.0-p3) is used to calculate the reads mapped to each gene.
Assembly: IMPLAD_EP_1.0
Supplementary files format and content: txt file includes raw counts for each Sample
Supplementary files format and content: txt file includes FPKM values for each Sample

organism: Epimedium pubescens

source_name: leaves

growth_protocol: These seedlings were transplanted into cultivation pots filled with a substrate mixture of river sand and perlite (3:2), and then cultured in a greenhouse. The light intensity was maintained at 2000 luX for 14 hours per day, and the temperature was controlled at 22 ± 2°C.

extract_protocol:
The total RNA of leaves was extracted using the RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (QIAGEN, Germany).
RNA liprares for RNA-sed were prepared usIng NEBNext® Ultra RNA Library Prep Kit for Illumina®

treatment_protocol: After 20 days of irrigation with 12.5% Hoagland nutrient solution for seedling recovery, seedlings with newly emerged roots and having resumed normal growth were subjected to different nitrogen levels: LN (nitrogen deficiency treatment, 0 mmol/L NO3-), MN (moderate nitrogen treatment, 7.5 mmol/L NO3-), and HN (excessive nitrogen treatment, 22.5 mmol/L NO3-).

value: leaves

tag: treatment

value: Excessive nitrogen

tag: time


title: GZLBM2022tissue155


title: GZLBM2022tissue160


title: Epimedium pubescens leaves,HN,48d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: P52* | 016 | TME

value: HNSCC

value: CR

tag: age

tag: Sex

value: Previous

value: NA mos


title: GZLBM2022tissue157

tag: disease state


title: GZLBM2022tissue158


title: GZLBM2022tissue153


title: Epimedium pubescens leaves,HN,48d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: GZLBM2022tissue152


title: P85* | 001 | TUMOUR

tag: bestresponse

value: PD

value: TRUE

tag: pathway

value: Nivolumab

value: Y

value: Male


title: P52* | 006 | TME

value: TME


title: Epimedium pubescens leaves,MN,48d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Moderate nitrogen


title: GZLBM2022tissue150

value: Lung adenocarcinoma


title: P52* | 004 | TME


title: GZLBM2022tissue149


title: P85* | 003 | TME

value: Never

value: 1 mos


title: P52* | 003 | TME


title: GZLBM2022tissue148


title: GZLBM2022tissue146


title: GZLBM2022tissue147


title: Epimedium pubescens leaves,MN,48,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Epimedium pubescens leaves,LN,48d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Nitrogen deficiency


title: P52* | 001 | TME


title: GZLBM2022tissue144


title: Epimedium pubescens leaves,LN,48d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: leaves


title: P260 | 011 | TME

value: Female

value: 0 mos


title: GZLBM2022tissue143


title: Epimedium pubescens leaves,LN,48d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: P260 | 010 | TME

value: HNSCC


title: Epimedium pubescens leaves,HN,36d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Excessive nitrogen


title: GZLBM2022tissue151


title: GZLBM2022tissue142


title: P260 | 009 | TME


title: Epimedium pubescens leaves,MN,48d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Nb_08

city: New Haven

first: Carla

last: Rothlin

state: CT

address: 300 Cedar Street

institute: Yale University

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 8

source_name: OT-II T cells

extract_protocol: Lysed in RLT lysis buffer diluted in water

treatment_protocol: Adoptively transferred CD45.2+CD4+ OT-II T cells were FACS-sorted from draining lymph nodes 4 days post immunization

tag: cell type

value: OT-II T cells

tag: infection status

value: Derived from N.b. infected hosts


title: GZLBM2022tissue141


title: Nb_05

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 5


title: Nb_07

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 7


title: Epimedium pubescens leaves,HN,36d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: P52* | 002 | TME

value: CR

value: TRUE

tag: mortality

tag: smokingstatus

value: Previous

value: NA mos


title: P260 | 008 | TME

value: PD

value: Nivolumab

value: Y

tag: pfs

tag: countofloweprgene

value: TME


title: GZLBM2022tissue145

value: Lung adenocarcinoma


title: Epimedium pubescens leaves,HN,36d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: Uninfected_04

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 4

value: Derived from uninfected hosts


title: GZLBM2022tissue140


title: P260 | 006 | TUMOUR

value: Never

tag: percentofloweprgene

tag: foi

value: TUMOUR


title: Epimedium pubescens leaves,MN,36d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: leaves

value: Moderate nitrogen


title: Uninfected_03

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 3


title: GZLBM2022tissue139


title: P260 | 005 | TUMOUR

value: HNSCC

value: Female

value: 0 mos

tag: responsesintumour

tag: responsesintme


title: Uninfected_02

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 2

value: OT-II T cells


title: GZLBM2022tissue138


title: P260 | 003 | TUMOUR

tag: tissue

value: TRUE


title: Epimedium pubescens leaves,MN,36d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

tag: treatment

tag: time


title: GZLBM2022tissue137


title: Epimedium pubescens leaves,MN,36d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: T2 old D6

city: Chicago

first: Shweta

last: Dipali

state: IL

address: 303 E. Superior St., Suite 10-220

institute: Northwestern University

description: 10X Genomics

data_processing:
Sixteen thousand cellswere loaded into the Chromium iX Controller on aChromium Next GEM Chip G,and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3’Reagent Kits v3.1 and Dual Index Kit TT Set A according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively.
FASTQ files were generated and demultiplexed from base call (.bcl) files using Cell Ranger from 10X Genomics. Cell Ranger was also used for alignment of the FASTQ files to the mouse reference genome (mm10) and to count the number of reads from each cell that align to each gene.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Ovary

extract_protocol:
Primary ovarian somatic cells were lifted from 2D monolayer culture or dissociated from organoids with 0.05% (monolayer) or 0.25% (organoids) trypsin. Trypsin was quenched with RPMI-1640 containing 10% FBS and 1% Penicillin-Streptomycin and the cell suspension was strained through a 40 µm cell strainer. Cells were pelleted by centrifugation at 500 x g for 5 min at room temperature, washed with DPBS containing 1% BSA, and resuspended in 100 µL DPBS containing 1% BSA. Cell number and viability were analyzed using a Nexcelom Cellometer Auto2000 with the AOPI fluorescent staining method.
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Ovary

value: Primary ovarian somatic cells

tag: strain

tag: age

value: 10-14 months

tag: time in_culture

value: Day 6 organoids


title: GZLBM2022tissue136

tag: disease state


title: T2 young D6

description: 10X Genomics

tag: cell type

value: 6-12 weeks


title: Epimedium pubescens leaves,LN,36d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Nitrogen deficiency


title: P808* | 011 | TME

tag: bestresponse

value: PR

tag: pathway

value: Nivolumab

value: N

tag: Sex

value: Male

value: Previous

value: NA mos

value: TME


title: T1 old D6

description: 10X Genomics


title: P808* | 010 | TME

value: HNSCC

tag: mortality

tag: smokingstatus

tag: pfs


title: P808* | 009 | TME

tag: countofloweprgene

tag: percentofloweprgene

tag: foi


title: GZLBM2022tissue135

value: Lung adenocarcinoma


title: GZLBM2022tissue134


title: Epimedium pubescens leaves,LN,36d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

tag: tissue

value: leaves


title: T2 old D1

description: 10X Genomics

value: Day 1 organoids


title: T2 young D1

description: 10X Genomics

value: Ovary


title: GZLBM2022tissue133


title: Epimedium pubescens leaves,HN,24d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

tag: treatment

value: Excessive nitrogen


title: P808* | 008 | TME

value: TRUE

tag: responsesintumour

tag: responsesintme


title: Epimedium pubescens leaves,HN,24d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

tag: time


title: P808* | 007 | TME

tag: age


title: GZLBM2022tissue132

tag: disease state


title: P808* | 006 | TUMOUR

value: TUMOUR


title: GZLBM2022tissue131


title: GZLBM2022tissue130


title: Epimedium pubescens leaves,HN,24d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: T2 old monolayer

description: 10X Genomics

tag: cell type

value: Primary ovarian somatic cells

tag: strain

value: 10-14 months

tag: time in_culture

value: 2D monolayer


title: Uninfected_01

description:
cell lysates were processed according to the manufacturer’s recommendations using the nCounter PanCancer Immune Profiling Panel and the nCounter system (NanoString Technologies). The data were subsequently analyzed using version 4.0 of the nSolverTM Analysis Software (NanoString Technologies) where the samples were normalized based on the panel of housekeeping genes as recommended by the manufacturer using the geoNorm algorithm 50.
SAMPLE 1

value: OT-II T cells

tag: infection status

value: Derived from uninfected hosts


title: T1 young D6

description: 10X Genomics

value: 6-12 weeks

value: Day 6 organoids


title: GZLBM2022tissue129


title: Epimedium pubescens leaves,MN,24d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Moderate nitrogen


title: P808* | 012 | TME

tag: bestresponse

value: PR

tag: pathway

value: Nivolumab

tag: mortality

value: N

tag: Sex

value: Male

value: Previous

value: NA mos

value: TME


title: Epimedium pubescens leaves,LN,36d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: leaves

value: Nitrogen deficiency


title: T1 old D1

description: 10X Genomics

value: Ovary

value: Primary ovarian somatic cells

value: Day 1 organoids


title: Epimedium pubescens leaves,MN,24d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: T2 young monolayer

description: 10X Genomics

value: 2D monolayer


title: T1 old monolayer

description: 10X Genomics

value: 10-14 months


title: P808* | 004 | TUMOUR

value: HNSCC

value: TRUE

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

value: TUMOUR


title: T1 young D1

description: 10X Genomics

tag: tissue

value: 6-12 weeks


title: P808* | 003 | TUMOUR

value: PR

value: Nivolumab

tag: foi

tag: responsesintumour

tag: responsesintme


title: P808* | 005 | TUMOUR

value: N

tag: age

value: Male


title: Epimedium pubescens leaves,MN,24d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

tag: treatment

value: Moderate nitrogen

tag: time


title: GZLBM2022tissue126

tag: disease state

value: Lung adenocarcinoma


title: GZLBM2022tissue127


title: T1 young monolayer

description: 10X Genomics

tag: cell type

tag: strain

tag: time in_culture


title: Epimedium pubescens leaves,LN,24d,rep C

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: leaves


title: P46 | 014 | TME

tag: bestresponse

value: PD

tag: pathway

tag: mortality

value: Y

value: Previous

value: 3 mos

value: TME


title: Epimedium pubescens leaves,LN,24d,rep A

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所

value: Nitrogen deficiency


title: Epimedium pubescens leaves,LN,24d,rep B

address: 马连洼街道马连洼北路151号

institute: 中国医学科学院药用植物研究所


title: GZLBM2022tissue125


title: Bulk ATAC-seq IR_D14_3

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

institute: Karolinska Institutet

description: ATAC-seq

data_processing:
ATAC-seq: Raw data were processed using Trimmomatic v0.36 by removing reads of low qualities and with a length of less than 30 nucleotides. The PCR duplicated reads were excluded using Picard (v2.20.4) tools after mapping to GRCh38 human reference genome using Bowtie2 (v2.3.5.1). The uniquely mapped reads were shifted and converted into bigwig format with a 200-bp extension size for IGV visualization using the deepTools. Peaks were called on each sample individually using MACS2/3 (v2.2.6/v3.0.0b1) with the default parameter except for using-f BAMPE option. Peaks overlapping with the repetitive regions in ENCODE blacklist downloaded from UCSC Table Browser were filtered out using BEDTools suite.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Files contains the peaks of ATAC-seq.

source_name: skin

extract_protocol:
ATAC-seq was performed as described in Corces, M., et al. Nat Methods (2017). Briefly, after washing with cold PBS, fibroblasts were treated with lysis buffer to extract nuclei. The isolated nuclei were incubated for 30 minutes at 37°C in a 50 µl Tn5 transposase reaction mix (Illumina FC-121-1031). The transposed chromatin was purified with Zymo DNA Clean & Concentrator (Zymo Research).
The ATAC-seq library preparation and sequencing were performed by Illumina NovaSeq 6000 SP-300 or NovaSeq X 10B-300 (2x150 bp) at the National Genomics Infrastructure at SciLifeLab Stockholm.

value: skin

value: Dermal fibroblast

tag: Sex

value: Irradiated


title: GZLBM2022tissue124


title: GZLBM2022tissue123


title: WT mouse 2

city: Shanghai

first: Xiangdong

last: Yang

address: Xietu Road

institute: Zhongshan Hospital Affiliated to Fudan University

data_processing:
The quality of raw sequencing reads post initial quality control (version 0.20.1) was evaluated using FastQC (version 0.11.9), followed by quantification of gene expression levels through alignment to the reference genome using HISAT2 (version 2.1.0) and analysis with HTSeq-count (version 0.11.2). Clean reads were mapped to the GRCm39 mouse reference genome using STAR (version 2.7.11b) to generate the expression count matrix. The counts matrix was converted into FPKM values to normalize the RNA-Seq data for gene length and sequencing depth. The FPKM matrix was imported into R and analyzed using the DESeq2 package (version 1.22.2) to normalize the data and estimate dispersion. Determinants of DEG were those with a p-value < 0.05 and a log2 fold change > 1. Ultimately, the analysis of KEGG pathway enrichment was conducted using the cluster Profiler package (version 4.13.0) in R.
Assembly: GRCm39
Supplementary files format and content: a csv file contains fpkm and annotation of genes

source_name: Hind limb skeleton muscle

extract_protocol:
The total RNA of muscles 3 days after surgery from WT and Hdc-/- mice was extracted using TRIzol reagent (Takara) for RNA-seq analysis.
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (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.

value: Hind limb skeleton muscle

value: HLI


title: Bulk ATAC-seq IR_D14_2

description: ATAC-seq


title: GZLBM2022tissue128


title: P46 | 013 | TUMOUR

value: HNSCC

value: TRUE

value: Nivolumab

tag: smokingstatus

tag: pfs

tag: countofloweprgene

value: TUMOUR


title: GZLBM2022tissue122

value: Lung adenocarcinoma


title: WT mouse 1

tag: tissue


title: Bulk ATAC-seq IR_D14_1

description: ATAC-seq


title: P46 | 008 | TME

value: Male

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: Bulk ATAC-seq Ctr_D14_3

description: ATAC-seq

tag: age

tag: treatment

value: Non-irradiated


title: P808* | 002 | TUMOUR

value: PR

value: N

value: NA mos

tag: responsesintme


title: HDCKO mouse 3


title: P46 | 009 | TME

value: PD

value: Y

value: Previous

value: 3 mos

value: TME


title: GZLBM2022tissue121

tag: disease state


title: GZLBM2022tissue120


title: Bulk ATAC-seq Ctr_D14_2

description: ATAC-seq

value: skin

tag: cell type

value: Dermal fibroblast


title: HDCKO mouse 1

value: Hind limb skeleton muscle

value: HLI


title: P46 | 007 | TME

value: HNSCC

value: TRUE

value: Nivolumab


title: Bulk ATAC-seq Ctr_D14_1

description: ATAC-seq


title: RNA, Tomato Negative PT

city: Villejuif

first: Garett

last: Dunsmore

address: 114 rue Edouard Vaillant

institute: Gustave Roussy

data_processing:
Raw counts were aligned to the GRCm38 mm10 Mus musculus genome from the Genome Reference Consortium using STAR 2.5.3a
Assembly: GRCm38 mm10
Supplementary files format and content: .csv
Supplementary files format and content: Counts

source_name: Pancreas Tumor

extract_protocol:
Mice were sacrificed and organs were harvested immediately. Tumors were visually identified, separated from other tissues (peritoneal membrane and spleen), and preserved in ice-cold PBS until digestion. Freshly harvested pancreas/tumors were cut into small pieces and digested in 2 ml of Dulbecco’s Modified Eagle Media (DMEM) supplemented with 10% fetal bovine serum and Collagenase type IV (Sigma) at a working concentration of 0.2mg/ml. Following 30 minutes of incubation at 37°C with 5% CO2, tissues were homogenized by passing multiple times through a 5ml syringe with an 18G needle. Cell suspensions were finally passed through a 70-micron filter before downstream analysis.
Briefly, cells were loaded onto a Chromium Next GEM Chip G, and single cell suspensions in gel beads-in-emulsion (GEMs) were generated using the chromium controller (10X genomics). Reverse transcription (RT) was performed to generate cDNA, which was amplified, cleaned, and fragmented. Finally, libraries were subjected to standard quality control (QC) steps before sequencing.

value: Pancreas Tumor

tag: genotype

value: MS4A3cre x RosaTdTomato


title: WT mouse 3


title: RNA, Tomato Positive PT


title: Bulk ATAC-seq RS49 RT- S+

description: ATAC-seq

value: Female

value: Surgery


title: P46 | 006 | TUMOUR

tag: bestresponse

value: Male

value: TUMOUR


title: P46 | 010 | TUMOUR

value: PD

tag: pathway

value: Y


title: GZLBM2022tissue118

value: Lung adenocarcinoma


title: GZLBM2022tissue119


title: GZLBM2022tissue117


title: RNA, CD45 Negative PT


title: P46 | 004 | TUMOUR

tag: mortality

value: Previous

value: 3 mos


title: HDCKO mouse 2


title: P46 | 005 | TME

tag: Sex

value: TME


title: Bulk ATAC-seq RS48 RT- S+

description: ATAC-seq

value: skin

value: Dermal fibroblast


title: GZLBM2022tissue115


title: Bulk ATAC-seq RS48 RT- S-

description: ATAC-seq

value: nonSurgery


title: RNA, Tomato Positive PERT

value: MS4A3creERT2 x RosaTdTomato


title: RNA, CD45 Negative PERT


title: GZLBM2022tissue114


title: RNA, Tomato Negative PERC

source_name: Pancreas

value: Pancreas


title: P94 | 012 | TME

value: HNSCC

value: TRUE

value: Nivolumab

tag: smokingstatus

value: Never


title: Bulk ATAC-seq RS47 RT- S-

description: ATAC-seq

value: Female


title: GZLBM2022tissue113


title: P94 | 011 | TME

tag: pfs


title: P46 | 001 | TUMOUR

value: Male

tag: countofloweprgene

value: TUMOUR


title: RNA, Tomato Negative PERT

tag: tissue

value: Pancreas Tumor


title: RNA, Tomato Positive PERC


title: GZLBM2022tissue112

value: Lung adenocarcinoma


title: Bulk ATAC-seq RS49 RT- S-

description: ATAC-seq


title: P94 | 009 | TME

value: PD

value: Y

tag: percentofloweprgene


title: P94 | 010 | TME

value: 3 mos

tag: foi

value: TME


title: GZLBM2022tissue116


title: P46 | 003 | TUMOUR

value: Previous

tag: responsesintumour


title: P94 | 008 | TME

tag: age


title: M3(metformin treated), replicate3, RNAseq

city: Kannapolis

first: Xiaohe

state: North Carolina

address: 500 Laureate Way

institute: North Carolina Central University

data_processing:
Before analysing the data, it is first necessary to ensure that these Reads are of sufficiently high quality to ensure the accuracy of the subsequent analyses. We carry out strict quality control of raw data with filtering criteria:(1) Remove Reads containing connectors;(2) Removal of low-quality Reads (including Reads with greater than 10% of N removed; Reads with more than 50% of the entire Read in the number of bases with a quality value
The HISAT2 software was used to quickly and accurately compare the Clean Reads with the reference genome to obtain the positioning information of the Reads on the reference genome.
Use StringTie to assemble the reads and reconstruct the transcriptome for subsequent analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files included raw count for each sample
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Mammary

growth_protocol: Female FVB/N mice were treated with metformin or saline starting from 8 weeks of age

extract_protocol:
Total RNA was extracted from mice of each group after 10 weeks of treatment with trizol.
The purity, concentration and integrity of extracted Total RNA were tested (NanoDrop 2000 spectrophotometer: to detect the purity and concentration of RNA; Agient2100/LabChip GX assay: to accurately detect the integrity of RNA), and after the samples were tested and qualified, library construction was carried out, and the main processes were as follows:(1) Enrich eukaryotic mRNA with magnetic beads with Oligo (dT);(2) Add Fragmentation Buffer to interrupt the mRNA randomly;(3) Synthesis of the first cDNA strand and double strand using mRNA as template and cDNA purification;(4) The purified double-stranded cDNA was then subjected to end repair, addition of A-tail and ligation of sequencing junctions, followed by fragment size selection with AMPure XP beads;(5) Finally, the cDNA library was enriched by PCR. After the library was constructed, Qubit 3.0 Fluorescence Quantification Instrument was used for the preliminary quantification, and the concentration should be more than 1ng/ul. Subsequently, Qsep400 High-Throughput Analysis System was used for the detection of insertion fragments in the library, and after the insertion fragments were in accordance with the expectation, Q-PCR was used to accurately quantify the effective concentration of the library (the effective concentration of the library was more than 2nM) to ensure the quality of the library.

treatment_protocol: The mice were administered 200 mg/kg/day of metformin via i.p. injection from 8 to 18 weeks of age

value: Mammary

value: Heterogenous mammary cells

value: WT

tag: treatment

value: 200 mg/kg/day Metformin I,p. between week 8 and week18


title: P46 | 002 | TME

value: HNSCC

value: TRUE

tag: responsesintme


title: GZLBM2022tissue108

tag: disease state


title: Bulk ATAC-seq RS47 RT- S+

description: ATAC-seq

value: skin

tag: cell type

value: Dermal fibroblast

value: Surgery


title: GZLBM2022tissue111


title: RNA, CD45 Negative PERC

value: Pancreas

tag: genotype

value: MS4A3creERT2 x RosaTdTomato


title: GZLBM2022tissue109

value: Lung adenocarcinoma


title: M2(metformin treated), replicate2, RNAseq


title: Control3, replicate3, RNAseq

value: saline


title: P94 | 006 | TUMOUR

tag: bestresponse

value: PD

value: Nivolumab

value: Y

value: Female

value: Never

value: TUMOUR


title: GZLBM2022tissue107


title: P19* | 012 | TME

tag: pathway

value: Male

value: 3 mos

value: TME


title: Control1, replicate1, RNAseq

value: Mammary

value: Heterogenous mammary cells

value: WT


title: GZLBM2022tissue105


title: M1(metformin treated), replicate1, RNAseq

value: 200 mg/kg/day Metformin I,p. between week 8 and week18


title: GZLBM2022tissue106


title: P19* | 011 | TME

value: HNSCC

value: TRUE

tag: mortality


title: Control2, replicate2, RNAseq


title: P94 | 001 | TUMOUR

tag: Sex


title: GZLBM2022tissue104

value: Lung adenocarcinoma


title: non-Germinal center B-cells, S1PR4 KO, replicate 3

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

institute: National Institutes of Health

data_processing:
raw reads were trimmed for adapters and low-quality bases using Cutadapt v2.10
alignment to the mouse reference genome (mm10) and the Gencode Release M30 annotation using STAR v2.5.3 in two-pass mode
PCR duplicates were marked using Picard MarkDuplicates v2.27.3
gene-level quantification was performed using RSEM v1.3.0
pairwise differential expression was performed using DESeq2
Assembly: mm10/Gencode M30
Supplementary files format and content: raw counts matrix

source_name: non-germinal center B-cells

growth_protocol: S1pr4−/−mice andS1pr4+/+mice (referred to as wildtype, WT) were originally obtained from The Jackson Laboratory (Bar Harbor, Maine) (strain B6.129P2-S1pr4tm1Dgen/J) and subsequently backcrossed to C57/BL6 at least 10 times. The S1PR4 colony was maintained within a Taconic Biosciences barrier facility (Germantown, NY).  Mice were transferred two weeks prior to the initiation of the experiments to a vivarium of the National Institute of Allergy and Infectious Diseases (NIAID), accredited by the American Association for the Accreditation of Laboratory Animal Care (AAALAC). Male and female mice, aged between 8-12 weeks old, were used for experiments with WT littermates serving as controls.

extract_protocol:
Freshly sorted cell populations were resuspended and stored in RNAprotect Cell Reagent (Qiagen) and subsequently RNA was isolated using a RNeasy Micro Kit (Qiagen).  RNA quality and purity was confirmed with a 2100 Bioanalyzer (Agilent).
Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: Anesthetized mice were immunized in the hind footpad using a 26- or 30-gauge needle with 20 µL of a Freund’s Incomplete Adjuvant (IFA) emulsion (InvivoGen) containing 50 µg ovalbumin (OVA, Biosearch Technologies) and 5 µg lipopolysaccharide (LPS, E. coli O111:B4, MilliporeSigma) to induce a robust TH1 immune response. Briefly, a solution of 0.5 mg/mL LPS and 5 mg/mL OVA in sterile PBS was combined 1:1 with IFA by passing between two borosilicate glass syringes affixed to a three-way stopcock until a stable emulsion was achieved.  Animals were euthanized at various timepoints after immunization, and the draining popliteal lymph nodes (dLN) collected for further processing.  In some experiments, the non-draining contralateral LN was used as a control.

value: non-germinal center B-cells

tag: strain

value: S1PR4 KO


title: non-Germinal center B-cells, S1PR4 KO, replicate 4

department: National Institute of Allergy and Infectious Diseases


title: GZLBM2022tissue110


title: P19* | 010 | TME

value: PD

value: Nivolumab

tag: smokingstatus

tag: pfs


title: P19* | 009 | TME

tag: tissue

value: Y

tag: countofloweprgene


title: GZLBM2022tissue100


title: non-Germinal center B-cells, replicate 4


title: GZLBM2022tissue102


title: GZLBM2022tissue103


title: non-Germinal center B-cells, S1PR4 KO, replicate 1


title: non-Germinal center B-cells, replicate 5


title: GZLBM2022tissue099


title: GZLBM2022tissue101


title: P19* | 007 | TME

value: Never

tag: percentofloweprgene

tag: foi


title: P19* | 006 | TUMOUR

tag: age

tag: responsesintumour

value: TUMOUR


title: P94 | 002 | TUMOUR

value: Female

tag: responsesintme


title: GZLBM2022tissue098

tag: disease state


title: non-Germinal center B-cells, S1PR4 KO, replicate 2

tag: cell type


title: P19* | 008 | TME

value: Male

value: 3 mos


title: P19* | 004 | TUMOUR


title: non-Germinal center B-cells, replicate 2

tag: genotype


title: non-Germinal center B-cells, replicate 3


title: GZLBM2022tissue097


title: GZLBM2022tissue096


title: non-Germinal center B-cells, replicate 1


title: P19* | 002 | TUMOUR

tag: bestresponse


title: GZLBM2022tissue095


title: GZLBM2022tissue094


title: Germinal center B-cells, S1PR4 KO, replicate 5

source_name: Germinal center B-cells

value: Germinal center B-cells


title: P19* | 001 | TUMOUR

tag: pathway


title: P19* | 005 | TUMOUR

tag: mortality


title: Germinal center B-cells, S1PR4 KO, replicate 4


title: P84 | 011 | TME

tag: Sex

value: Previous

value: 5 mos

value: TME


title: GZLBM2022tissue092


title: Germinal center B-cells, S1PR4 KO, replicate 3

tag: strain


title: P84 | 010 | TME

value: HNSCC

tag: smokingstatus


title: GZLBM2022tissue091


title: P84 | 009 | TME

value: TRUE

tag: pfs


title: Germinal center B-cells, S1PR4 KO, replicate 2


title: GZLBM2022tissue090

value: Lung adenocarcinoma


title: GZLBM2022tissue093


title: Germinal center B-cells, replicate 6

value: WT


title: Germinal center B-cells, S1PR4 KO, replicate 1

value: S1PR4 KO


title: P19* | 003 | TUMOUR

tag: tissue

value: PD


title: P84 | 008 | TME

value: Nivolumab

tag: countofloweprgene


title: GZLBM2022tissue089


title: Germinal center B-cells, S1PR4 KO, replicate 6


title: P84 | 007 | TME

value: Y

tag: percentofloweprgene


title: Germinal center B-cells, replicate 5


title: GZLBM2022tissue088


title: P84 | 004 | TUMOUR

tag: foi


title: GZLBM2022tissue087


title: P84 | 005 | TUMOUR

tag: age


title: P84 | 006 | TUMOUR

tag: responsesintumour


title: Germinal center B-cells, replicate 3


title: Germinal center B-cells, replicate 4


title: P84 | 003 | TUMOUR

tag: responsesintme


title: GZLBM2022tissue085

tag: disease state


title: P84 | 001 | TUMOUR


title: Germinal center B-cells, replicate 2

tag: cell type


title: GZLBM2022tissue084


title: P79* | 012 | TME

value: Never


title: non-Tfh CD4 T-cells, S1PR4 KO, replicate 5

source_name: CD4+ non-Tfh cells

value: CD4+ non-Tfh cells

tag: genotype


title: GZLBM2022tissue083


title: GZLBM2022tissue082


title: GZLBM2022tissue081


title: non-Tfh CD4 T-cells, S1PR4 KO, replicate 6


title: P79* | 011 | TME

tag: bestresponse


title: non-Tfh CD4 T-cells, S1PR4 KO, replicate 4


title: non-Tfh CD4 T-cells, S1PR4 KO, replicate 2


title: P79* | 010 | TME

tag: pathway


title: GZLBM2022tissue080


title: GZLBM2022tissue078


title: P79* | 008 | TME

tag: mortality


title: P79* | 009 | TME

tag: Sex


title: GZLBM2022tissue086


title: P79* | 007 | TME


title: non-Tfh CD4 T-cells, replicate 6

tag: strain


title: GZLBM2022tissue079


title: non-Tfh CD4 T-cells, S1PR4 KO, replicate 1


title: P79* | 005 | TUMOUR

tag: smokingstatus

value: TUMOUR


title: non-Tfh CD4 T-cells, S1PR4 KO, replicate 3


title: Germinal center B-cells, replicate 1


title: GZLBM2022tissue077


title: P79* | 006 | TUMOUR

value: Male

tag: pfs


title: non-Tfh CD4 T-cells, replicate 4


title: non-Tfh CD4 T-cells, replicate 5


title: GZLBM2022tissue076


title: P79* | 004 | TUMOUR

tag: tissue

value: 3 mos


title: P79* | 002 | TUMOUR

tag: countofloweprgene


title: P79* | 003 | TUMOUR

tag: percentofloweprgene


title: GZLBM2022tissue075


title: GZLBM2022tissue072


title: GZLBM2022tissue074


title: non-Tfh CD4 T-cells, replicate 1


title: GZLBM2022tissue070


title: GZLBM2022tissue073


title: GZLBM2022tissue071


title: Tfh CD4 T-cells, S1PR4 KO, replicate 5

source_name: CD4+ Tfh cells

value: CD4+ Tfh cells


title: non-Tfh CD4 T-cells, replicate 2


title: Tfh CD4 T-cells, S1PR4 KO, replicate 6


title: GZLBM2022tissue069


title: P79* | 001 | TUMOUR

tag: foi


title: P818* | 009 | TME

tag: age

value: Previous

value: 29 mos


title: P818* | 012 | TME

tag: responsesintumour

value: TME


title: Tfh CD4 T-cells, S1PR4 KO, replicate 3


title: P818* | 010 | TME

value: HNSCC

tag: responsesintme


title: GZLBM2022tissue068

tag: disease state


title: Tfh CD4 T-cells, S1PR4 KO, replicate 2

tag: cell type


title: Tfh CD4 T-cells, S1PR4 KO, replicate 4

tag: genotype


title: P818* | 007 | TME

tag: bestresponse

value: TRUE


title: non-Tfh CD4 T-cells, replicate 3


title: GZLBM2022tissue067

value: Lung adenocarcinoma


title: Tfh CD4 T-cells, S1PR4 KO, replicate 1


title: P818* | 008 | TME

tag: pathway


title: siCT-CTCF-High_rep2

city: Boston

first: Kashish

last: Chetal

state: MA

address: 55 Fruit St

department: Molecular biology

institute: MGH

description: Control CTCF High replicate 2

data_processing:
Sequencing reads were aligned against the hg19 reference genome using BWA (PMID: 20080505). Alignments were filtered for uniquely mapped reads and duplicates were removed.
ChIP over Input ratio coverage tracks were generated using deepTools (PMID: 27079975).
Peaks were called using HOMER (PMID: 20513432) with default parameters.

source_name: RPE

extract_protocol:
Cells were fixed with 1% formaldehyde for 13 minutes. After quenching and cell lysis, chromatin was sonicated using a Q800R3 sonicator (QSonica).
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Library Preparation Kit Set A and B with associated index barcode adapters. 1 ng or 30µL of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were cleaned up using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity D1000 DNA Kit.

tag: cell line

value: RPE

value: Retinal pigment epithelial

tag: antibody

value: CTCF

tag: treatment

value: siRNA Knockdown


title: siCT-INPUT_rep1

description: Control input replicate 1

value: input


title: GZLBM2022tissue065


title: GZLBM2022tissue066


title: P818* | 011 | TME

value: PD

value: Nivolumab

tag: mortality

value: Y

tag: Sex

tag: smokingstatus


title: Tfh CD4 T-cells, replicate 6

tag: strain

value: WT


title: Tfh CD4 T-cells, replicate 4


title: siCT-CTCF-High_rep1

description: Control CTCF High replicate 1


title: Tfh CD4 T-cells, replicate 5


title: siCT-INPUT_rep2

description: Control input replicate 1


title: siKDM3B_58-CTCF-High_rep2

description: siKDM3b (#57) CTCF High replicate 2


title: Tfh CD4 T-cells, replicate 3


title: siKDM3B_58-INPUT_rep2

description: siKDM3b (#58) input replicate 1


title: P818* | 003 | TUMOUR

tag: tissue

value: Male

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

value: TUMOUR


title: Tfh CD4 T-cells, replicate 2

value: CD4+ Tfh cells


title: P818* | 004 | TUMOUR

tag: age

value: Previous

value: 29 mos

tag: foi

tag: responsesintumour

tag: responsesintme


title: GZLBM2022tissue062

tag: disease state


title: P818* | 006 | TUMOUR

value: HNSCC

tag: bestresponse

tag: pathway


title: siKDM3B_57-CTCF-High_rep1

description: siKDM3b (#57) CTCF High replicate 1

tag: cell line

tag: cell type

tag: antibody


title: GZLBM2022tissue060


title: siKDM3B_57-INPUT_rep1

description: siKDM3b (#57) input replicate 1

tag: treatment


title: GZLBM2022tissue061


title: P29 | 023 | TME

value: SD

value: TRUE

tag: mortality

tag: Sex

value: Female

tag: smokingstatus

value: Current

value: 9 mos

value: TME


title: GZLBM2022tissue059

value: Lung adenocarcinoma


title: GZLBM2022tissue064


title: FVB/N lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample C

city: OXFORD

first: Anil

last: Upreti

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

data_processing:
Raw reads were quality-analyzed using FastQC and MultiQC .
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cut adapt and trim galore with paramaters -q 20 --phred33 --length 20.
Trimmed sequence reads were mapped to GrCM39 using Hisat2 incorporating splice juncation from genecode GTF .
Gene counts were generated using Stringtie2.1.5
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: Normalized gene count matrix from DESeq2

source_name: Lens Epithelium

growth_protocol: Lens epitheliall explants were maintained in 35mm culture dish with pre-calibrated M-199 media supplemented with 1% antibiotic-antimycotic solution and 0.1% bovine serum albumin  diluted  to 50% concentration, with vitreous henceforth referred to as “differentiation medium (DM)”, for 1 day or 5 days or 10 days at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNEasy Mini Kit (Qiagen cat. 74104) following the manufacturer’s instructions.
RNA libraries were constructed by Novogene (Sacramento, CA, USA) using a TruSeq (Illumina) library prep kit.

tag: tissue

value: Lens Epithelium

tag: genotype

value: FVB/N


title: P29 | 024 | TME

value: Nivolumab

value: Y

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: FVB/N lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample B


title: MUT4_BTY

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against the GRCm38.99 transcriptome using RSEM.
Estimated counts calculated by RSEM were normalized with the EdgeR package from Bioconductor, using the TMM method.
Assembly: GRCm38.99
Supplementary files format and content: Ensembl gene ID, gene name, and normalized counts for 14,608 genes, in each sample, for the collection of genes with more than 1 CPM in at least four samples.

source_name: OFT

extract_protocol:
RNA was harvested using Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific)
Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated, followed by second strand removal, uracil excision from the adaptor, and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher)

value: OFT

value: Mib1V943F/+ Gata6STOP/+


title: GZLBM2022tissue058

city: Toronto

first: Vikas

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded or fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles


title: MUT3_BTY


title: GZLBM2022tissue057


title: MUT2_BTY


title: FVB/N lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample A


title: P29 | 021 | TME

source_name: HNSCC

tag: age

tag: foi

tag: responsesintumour


title: P818* | 005 | TUMOUR

tag: bestresponse

value: PD

value: Male

tag: responsesintme

value: TUMOUR


title: Pten knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample C

value: Pten knockout in FVB/N background


title: Tfh CD4 T-cells, replicate 1

value: CD4+ Tfh cells

tag: strain

value: WT


title: MUT1_BTY


title: GZLBM2022tissue056

source_name: Lung adenocarcinoma

tag: disease state


title: Pten knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample B


title: WT4_BTY

value: Control


title: P29 | 020 | TUMOUR

value: HNSCC

value: SD

value: TRUE

tag: pathway

value: Female

value: Current


title: Pten knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample A

value: Lens Epithelium

tag: treatment


title: P29 | 019 | TUMOUR

value: Nivolumab

tag: mortality

value: 9 mos


title: P29 | 018 | TUMOUR

value: Y

tag: Sex


title: P818* | 001 | TUMOUR

tag: smokingstatus

value: Previous

value: 29 mos


title: WT2_BTY

tag: tissue

value: OFT


title: Pten knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample C

tag: genotype


title: GZLBM2022tissue053

value: Lung adenocarcinoma


title: Pten knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample B

value: Pten knockout in FVB/N background


title: WT1_BTY


title: GZLBM2022tissue052


title: P29 | 017 | TUMOUR

tag: pfs

value: TUMOUR


title: Pten knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample A


title: GZLBM2022tissue051


title: U251 treated with LLY-283, biological replicate 4

first: Uma

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

description:
LLY_S8
mRNA-seq

data_processing:
Basecalling software : RTA 3.10.30
Demultiplexing Software : Bcl2fastq v2.20
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt 1.18 before alignment with the reference genome (Human_hg38) and the annotated transcripts using STAR 2.7.0f.
Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility 2.18.26.
In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools 1.3.1.
Assembly: hg38
Supplementary files format and content: RSEM_genes_normalized_tpm_counts.tsv

growth_protocol: U251 cell line was grown in DMEM supplemented with 10% FBS (Invitrogen).

extract_protocol:
RNA was extracted using the RNeasy mini kit from QIAGEN. DNA digestion was performed on column using DNase.
200 ng of RNA was used as input for mRNA capture with oligo-dT coated magnetic beads. The mRNA was fragmented, followed by random-primed cDNA synthesis. The resulting double-stranded cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification to generate a sequencing ready library.

treatment_protocol: U251 cells were treated with either DMSO or LLY-283 (100nM) for 24hours before the extraction.

tag: cell line

value: WT


title: Pten knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample C


title: P29 | 016 | TUMOUR

tag: countofloweprgene

tag: percentofloweprgene


title: GZLBM2022tissue050

last: Patil

address: 610 University Ave.

institute: Princess Margaret Cancer Center

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.


title: WT3_BTY

value: Control


title: U251 treated with LLY-283, biological replicate 3

description:
LLY_S7
mRNA-seq


title: U251 treated with LLY-283, biological replicate 2

description:
LLY_S6
mRNA-seq


title: GZLBM2022tissue054


title: P29 | 014 | TUMOUR

value: HNSCC

tag: age

tag: foi


title: GZLBM2022tissue049


title: P29 | 015 | TUMOUR

tag: bestresponse

value: SD

tag: responsesintumour


title: P29 | 013 | TUMOUR

value: TRUE

tag: responsesintme


title: Pten knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample A


title: P29 | 012 | TUMOUR

value: Female


title: U251 treated with LLY-283, biological replicate 1

description:
LLY_S5
mRNA-seq


title: GZLBM2022tissue048

tag: disease state


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample C

value: Fgfr 1-3 and Pten knockout in FVB/N background


title: GZLBM2022tissue047


title: U251 treated with DMSO, biological replicate 4

description:
Veh_S4
mRNA-seq

value: Vehicle


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample B

value: Lens Epithelium


title: GZLBM2022tissue046


title: P29 | 010 | TUMOUR

tag: pathway

value: Nivolumab

value: Current

value: 9 mos


title: GZLBM2022tissue055


title: P29 | 011 | TUMOUR

value: Y


title: Pten knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample B

tag: treatment


title: P818* | 002 | TUMOUR

value: PD

tag: mortality

value: Male

value: Previous

value: 29 mos


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample A


title: U251 treated with DMSO, biological replicate 3

description:
Veh_S3
mRNA-seq

value: WT


title: U251 treated with DMSO, biological replicate 2

description:
Veh_S2
mRNA-seq


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample C


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample B


title: GZLBM2022tissue063

value: Lung adenocarcinoma


title: GZLBM2022tissue045


title: GZLBM2022tissue043


title: U251 treated with DMSO, biological replicate 1

description:
Veh_S1
mRNA-seq


title: GZLBM2022tissue044


title: GZLBM2022tissue042


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample A


title: Tek Alleles_frequency

city: Wuhan city

first: Qian

last: Chen

address: No.299 bayi road, wuchang district

institute: Wuhan University

data_processing:
Thecleandatawasgeneratedbytrimminglowqualitybasesatbothendsofreadandremoveshortfragments,thisworkwascompletedbysequencingcompany
For deep-seq, the data was handled by CRISPRessoPooled
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: txt files include DNA sequences for each sample

source_name: embryonic kidney

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

value: embryonic kidney

tag: cell type

value: Epithelial cells

value: wild type

value: Target deep sequence


title: P29 | 007 | TME

value: HNSCC

value: SD

value: TRUE

tag: Sex

value: Female

tag: smokingstatus

value: TME


title: P29 | 008 | TME

tag: tissue

value: Nivolumab

value: Current

value: 9 mos


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample C

value: Lens Epithelium

tag: genotype

value: Fgfr 1-3 and Pten knockout in FVB/N background


title: P29 | 009 | TUMOUR

value: Y

tag: pfs

value: TUMOUR


title: GZLBM2022tissue041

value: Lung adenocarcinoma


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample B


title: GZLBM2022tissue040


title: CQLb2_identifiedOfftargets

data_processing:
Thecleandatawasgeneratedbytrimminglowqualitybasesatbothendsofreadandremoveshortfragments,thisworkwascompletedbysequencingcompany
Forguide-seq,thesequencingdatawasprocessedbycorrespondingsoftwarenamedguideseq,the human genome version used in the analysis is hg19;
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: txt files include DNA sequences for each sample

value: embryonic kidney

tag: cell line

value: Guide seq


title: P29 | 005 | TME

tag: countofloweprgene

tag: percentofloweprgene


title: Fgfr 1-3 and Pten knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample A


title: GZLBM2022tissue039


title: Fgfr 1-3 knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample C

value: Fgfr 1-3 knockout in FVB/N background


title: CQCe_identifiedOfftargets

value: Epithelial cells

value: wild type


title: P29 | 004 | TME

value: HNSCC

value: SD

tag: age

tag: foi


title: CQAs_identifiedOfftargets


title: P29 | 006 | TME

tag: bestresponse

value: TRUE

value: Female

tag: responsesintumour


title: Fgfr 1-3 knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample B


title: Brain, Wildtype, N-PPG, 71

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 291 Campus Dr

institute: Stanford Medicine

description: library name: 71

data_processing:
Per Genewiz standard data processing pipe, 2020
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA sent to Genewiz

value: Brain

value: all brain

value: Wildtype

value: N-PPG

tag: time

value: Day of demise


title: GZLBM2022tissue038

tag: disease state


title: GZLBM2022tissue037


title: Pdg Alleles_frequency

tag: treatment

value: Target deep sequence


title: Brain, Wildtype, N-PPG, 70

description: library name: 70


title: Fgfr 1-3 knockout lens epithelial explants, 10 days in  differentiation media +24 hrs in culture media sample A

value: Lens Epithelium


title: GZLBM2022tissue035

value: Lung adenocarcinoma


title: Pde Alleles_frequency

value: embryonic kidney


title: P60 | 012 | TME

value: PD

tag: pathway

value: Nivolumab

tag: mortality

value: Y

value: Male

value: Previous

value: 3 mos

value: TME

tag: responsesintme


title: Fgfr 1-3 knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample C

value: Fgfr 1-3 knockout in FVB/N background


title: Brain, Wildtype, no N-PPG, 69

description: library name: 69

value: Brain

tag: cell type

value: no N-PPG


title: GZLBM2022tissue036


title: P29 | 001 | TME

tag: tissue

value: HNSCC

value: SD

value: TRUE

tag: Sex

value: Female

tag: smokingstatus

value: Current

value: 9 mos


title: P60 | 011 | TME

tag: pfs


title: P60 | 010 | TME

tag: countofloweprgene


title: Brain, Wildtype, no N-PPG, 68

description: library name: 68

value: all brain

tag: genotype

value: Wildtype

value: Day of demise


title: Fgfr 1-3 knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample A

value: Lens Epithelium


title: GZLBM2022tissue034

value: Lung adenocarcinoma


title: Fgfr 1-3 knockout lens epithelial explants, 5 days in  differentiation media +24 hrs in culture media sample B


title: P29 | 003 | TME

value: Nivolumab

value: Y

tag: age

tag: percentofloweprgene


title: P29 | 002 | TME

tag: bestresponse

tag: foi

value: TME


title: GZLBM2022tissue033


title: Brain, Wildtype, N-PPG, 67

description: library name: 67

value: N-PPG

tag: time


title: Brain, Wildtype, no N-PPG, 64

description: library name: 64

value: Brain


title: Fgfr 1-3 knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample C

value: Fgfr 1-3 knockout in FVB/N background


title: P60 | 009 | TME

value: HNSCC

value: PD

value: Male

value: Previous

value: 3 mos

tag: responsesintumour


title: P60 | 008 | TME

value: TRUE


title: GZLBM2022tissue032

tag: disease state


title: GZLBM2022tissue031


title: Brain, Wildtype, no N-PPG, 59

description: library name: 59

value: all brain

tag: treatment

value: no N-PPG


title: Brain, Wildtype, no N-PPG, 58

description: library name: 58

value: Wildtype

value: Day of demise


title: Fgfr 1-3 knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample A

value: Lens Epithelium


title: GZLBM2022tissue030

value: Lung adenocarcinoma


title: P60 | 007 | TUMOUR

tag: pathway

value: Nivolumab

tag: mortality

value: Y

value: TUMOUR


title: TKO_Rep3

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

description:
TKO_whole_lung_Rep3
Egln1 KO in Tie2+cells and FABP4-5 in all cells

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to mouse genome mm10 using STAR.
Reads were counted on the exons of mm10 genes using htseq.
Differential gene expression analysis was performed using edgeR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: lung

extract_protocol:
RNA was harvested using Zymo Research Quick-RNA Miniprep Kits with DNase I digestion.
Novogene performed the library construction using NEB library kit.

value: lung

value: Egln1Tie2Cre KO plus Fabp4-5 KO


title: GZLBM2022tissue029


title: TKO_Rep2

description:
TKO_whole_lung_Rep2
Egln1 KO in Tie2+cells and FABP4-5 in all cells


title: Brain, Huntington's, N-PPG, 15HT

description: library name: 15HT

value: Brain

tag: cell type

value: Huntington's

value: N-PPG


title: GZLBM2022tissue028


title: P60 | 006 | TUMOUR

first: Habib

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: tissue

value: HNSCC

value: PD

value: Male

value: Previous

tag: responsesintme