title: Fibroblasts, si-POSTN, B2

city: Shenzhen

first: Cong

last: Huang

state: Guangdong

address: No. 1120, Lianhua Road, Futian District

institute: Peking University Shenzhen Hospital

description: Library name: Sample 5

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

source_name: Keloid Fibroblasts

growth_protocol: Primary human dermal fibroblasts were isolated from tissues obtained from keloid patients as previously described (28). Firstly, the epidermis and adipose tissues were removed from the specimens of keloid patients. Then, the dermis was cut into small sections and allowed to attach to the 10 cm dish. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Total RNA was extracted from si-POSTN/si-CTL transfected Keloid fibroblasts using TRIzol reagent. Purified RNA was quantified using a NanoDrop 2000 (Thermo Scientific) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).CA, USA).
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Keloid fibroblasts were cultured to 70% confluent and then transfected with POSTN siRNAs and controls using Lipofectamine™ RNAiMAX Transfection Reagent (#13778150, Thermo Scientific) according to the manufacturer’s instruction.

value: Keloid Fibroblasts

value: wild type

value: si-POSTN


title: Fibroblasts, si-POSTN, B3

status: Public on Sep 10 2025

type: SRA

country: China

description: Library name: Sample 6

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: genotype

tag: treatment


title: HOM 3

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

description: Library name: Sample 7

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm39 whole genome using HISAT2 Version 2.1.0
FeatureCounts version 2.0.2 was used for counting reads to genes.
Differential expression analysis between genotypes was performed using the DESeq2 R package (2_1.6.3)
Assembly: mm39
Supplementary files format and content: tab-delimited file includes  the results of the differential expression analysis

organism: Mus musculus

source_name: Frontal cortex

extract_protocol:
Bulk RNA was extracted using Qiagen Lipid Tissue kit,  from frontal cortex, of wild type and homozygous TardbpM323K/M323K  male mice at 9-months of age (in an  F1 hybrid genetic background, C57BL/6J- DBA/2J). Quality and quantity was assessed using the 5400 Fragment Analyzer System (Agilent Technologies).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

tag: tissue

value: Frontal cortex


title: Fibroblasts, si-POSTN, B1

description: Library name: Sample 4


title: 1006-1

type: RNA

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

institute: GENVIP research group

hyb_protocol: Gene expression was evaluated through the nCounter MAX (NanoString Technologies) and the nCounter Host Response Panel, which includes 785 genes. We followed standard protocols; including 12 RNA hybridization with 5 ul of RNA as input, and hybridization time of 18 hours for all samples. We also mixed controls and ACD patient samples in the same runs to avoid technical sample bias and batch effects.

data_processing: We carried out a quality control (QC) of the raw expression data checking some technical parameters following manufacturer recommendations to verify the absence of technical problems. Samples that did not pass technical QC, or with low number of genes detected, were excluded for downstream analysis.   Genes with counts below the background (defined as the mean + 2 standard deviations [SD] of the negative control spikes in the code set, disregarding negative control C, which typically yields a higher number of counts) were excluded from both normalization and the differential expression analysis. After filtering out genes expressing below the background (maximum expression value < background), we detected a total of 566 and 672 genes (out of the total 785 in the NanoString panel) in ACD patients and healthy controls, respectively. In addition, 553 out of 566 genes in ACD and 648 out of 672 genes in healthy controls.  Data normalization was performed through an iterative strategy that combines both DESeq2 and RUVSeq packages. Control reference genes for data normalization were detected by selecting invariable genes (P-value > 0.1, BaseMean > 100 and |log2FC| < 0.2) after a naïve differential expression analysis between TP1 And TP2 in both ACD and healthy controls separately. Genes expressed below the background were removed. We used a paired-sampling design correcting by subject ID to carry out analysis of transcriptome differences before the musical stimuli (Pretest; time-point one or TP1) and after the musical stimuli (Posttest; TP2).

source_name: Saliva

extract_protocol: RNA from saliva was isolated using 500µl of sample and the RNeasy microkit (Qiagen). We slightly modified the protocol provided by the extraction kit as recommended by the Oragene tubes supplier. RNA concentration step and an additional DNase treatment were undertaken using an RNA clean & concentrator kit (Zymo Research). RNA amount and integrity were checked using TapeStation 4200 (Agilent), and DV200 values were calculated to ensure that >50% of the RNA fragments were above 200nt and to estimate the optimal sample input.

tag: phenotype

value: ACD

tag: timepoint

tag: gender

value: Female

tag: plate

tag: subject


title: Yeast, PolysomeProf, R3, 42C, NonDepl, Pool4

city: Basel

first: Attila

last: Becskei

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: Library name: GFB.15071_PolyProfNonDepl42rep34_S24

data_processing:
Sequence reads were trimmed for adaptor sequences using TrimGalore (TrimGalore v0.6.5) with --illumina parameter
Trimmed sequence reads were mapped and TPM values obtained with Salmon (Salmon v1.9.0)
Salmon index was created from NCBI's reference transcriptome (S288C, assembly R64) with Salmon index command
TPM quantification was performed with Salmon quant command
parameters: --validateMappings --seqBias --gcBias
Assembly: S288C, assembly R64
Supplementary files format and content: Microsoft excel spreadsheet with TPM values

organism: Saccharomyces cerevisiae BY4743

growth_protocol: S. cerevisiae BY strains were grown at 30°C in complete synthetic media (Complete Supplement: Formedium #DCS0019, Yeast Nitrogen Base: Formedium #CYN0410) (with 2% raffinose and 0.005% glucose) until the mid-log phase (OD600 = 0.6) at 30°C.

extract_protocol:
Cells were collected by addition of 1 volume of culture to 2 volumes of chilled medium (0°C) containing cycloheximide (CHX) (ThermoScientific #357420050) at 1.5x (150 µg/mL). The resulting mixture was immediately submerged in a -20°C bath (1:1 mix of ethanol and water) for two minutes (so that the final temperature is less than 10°C) The cells were spun down at 4000rpm (3000g) for 10min in a centrifuge at 4°C. The supernatant was removed and the pellet was immediately subjected to lysis. The cell lysis and gradient preparation was performed as previously described in Rahaman, et. al. Science Advances, 2023. For the ultracentrifugation, the A254 of the lysate was measured by mixing sample (or blank with Polysome Lysis Buffer) with water in a 1:20 volumetric ratio. 2-4 A254 unit equivalents of  the sample was loaded onto the 10-50% sucrose gradient. Ultracentrifugation was carried out with a SW41Ti rotor (swing bucket) at 40000rpm (equivalent to 275,000g) for 2h at 4°C. The polysome profile was generated with BioComp™ Polysome Profiling machine. 25 fractions (450µL each) corresponding to different positions in the centrifuge tube were collected. For RNA purification, the fractions were pooled according to the peaks of A254 polysome profile (free fraction, 40S, 60S, monosome, etc. and in-vitro transcribed spike-in RNAs were added to each pool to serve as a volumetric control. Subsequently, the pools were subjected to phenol-chloroform extraction (Phenol : chloroform : isoamyl-alcohol = 25:24:1). Precipitation was carried out with 2.5 volumes of ethanol at −80°C overnight with 2µL of GlycoBlue (ThermoScientific #AM9516) as co-precipitant. RNA was reconstituted with 20µL of nuclease free water (ThermoScientific #AM9932) containing RNasIN (Promega #N2611) at 1µL/mL (40U/mL). This RNA was further purified using RNeasy MinElute Cleanup Kit (Qiagen #74204) with on-column DNase digestion. The purified RNA was then used for RNA-Seq.
Stranded SMART-Seq (Takara)

treatment_protocol: For the standard temperature experiment, the cells growing at 30°C were sampled upon reaching the mid-log phase. For the heat-shock experiment, cells were transferred to a 42°C medium upon filtration with a 0.45µm filter and resuspension. They were grown for an additional 30 min before sampling.

tag: cell line


title: Yeast, PolysomeProf, R3, 42C, NonDepl, Pool3

description: Library name: GFB.15070_PolyProfNonDepl42rep3tri_S23


title: Yeast, PolysomeProf, R3, 42C, NonDepl, Pool2

description: Library name: GFB.15069_PolyProfNonDepl42rep3di_S22


title: Fibroblasts, si-CTL, A3

description: Library name: Sample 3

value: si-CTL


title: HOM 2

description: Library name: Sample 6


title: B4470-1

value: Male


title: HOM 1

description: Library name: Sample 5


title: Yeast, PolysomeProf, R3, 42C, NonDepl, Pool1

description: Library name: GFB.15068_PolyProfNonDepl42rep3mono_S21


title: Fibroblasts, si-CTL, A2

description: Library name: Sample 2


title: Wildtype 4

description: Library name: Sample 4

value: Wild type


title: Yeast, PolysomeProf, R2, 42C, NonDepl, Pool4

description: Library name: GFB.15067_PolyProfNonDepl42rep24_S20


title: Yeast, PolysomeProf, R2, 42C, NonDepl, Pool3

description: Library name: GFB.15066_PolyProfNonDepl42rep2tri_S19


title: B4591-1

value: CONTROL


title: 1006-2


title: Yeast, PolysomeProf, R2, 42C, NonDepl, Pool2

description: Library name: GFB.15065_PolyProfNonDepl42rep2di_S18


title: Wildtype 3

description: Library name: Sample 3


title: Yeast, PolysomeProf, R2, 42C, NonDepl, Pool1

description: Library name: GFB.15064_PolyProfNonDepl42rep2mono_S17


title: Yeast, PolysomeProf, R1, 30C, NonDepl, Pool4

description: Library name: GFB.15063_PolyProfNonDepl30rep14_S16


title: PRO-SEQ of shRFC3 cells rep2

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: Library name: shRFC3_2

library_source: other

data_processing:
(PRO-SEQ) Raw PRO-seq reads were processed as follows: Reads shorter than 15 bp were discarded. Reads aligning to ribosomal RNA (rRNA) were removed using Bowtie2 (--un-conc-gz). The remaining reads were then aligned to the human reference genome (hg38 assembly) using Bowtie2 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant. Strand-specific, single-base-pair resolution coverage tracks were generated in normalized BigWig format using the bamCoverage function from deepTools. The following parameters were applied for strand separation: Forward strand: --Offset 1 --samFlagInclude 82, Reverse strand: --Offset 1 --samFlagInclude 98.
Assembly: hg38
Supplementary files format and content: bigwig for PRO-SEQ
Library strategy: PRO-SEQ

molecule: other

source_name: liver

extract_protocol:
PRO-SEQ experiments, Nuclear run-on RNA was extracted using TRIzol LS reagent
PRO-SEQ: cells were washed twice with ice-cold PBS and then permeabilized by incubation in permeabilization buffer on ice for 10 minutes. Nuclei were subsequently washed twice with wash buffer and resuspended in 100 μl of freezing buffer. An equal volume of reaction buffer was added for the nuclear run-on reaction, which proceeded at 37°C for 7 min. Nuclear run-on RNA was extracted using TRIzol LS reagent (Invitrogen), following the manufacturer’s instructions, and precipitated with ethanol. The recovered RNA was then ligated to a 3' adaptor using T4 RNA ligase. Biotinylated RNA was captured by incubation with streptavidin beads (Smart-Lifescience) for 20 minutes. While immobilized on the beads, the RNA underwent sequential enzymatic repairs: (1) 5' hydroxyl repair, (2) decapping, and (3) 5' adaptor ligation. Following these repairs, RNA was eluted from the beads using TRIzol reagent. The eluted RNA was then reverse-transcribed and amplified by PCR to generate sequencing libraries. The final cDNA library was purified, size-selected, and sequenced on an Illumina HiSeq2000 platform.

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: B4470-2


title: HFF.1KPa.18hVer.rep3

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

country: USA

institute: Duke University

description: Library name: HFF.1KPa.18hVer.rep3

library_source: genomic

data_processing:
FastQC was used to identify read quality, and adapter reads were trimmed using Trimmomatic v0.32 followed by Bowtie alignment (v1.0) of the reads to the reference genome using the settings: -v 2 –best –strata -m 1 with duplicate reads removed using Picard MarkDuplicates (v1.13) and ENCODE hg38 blacklist reads removed using bedtools2 v2.25.
Peak calling was performed using MACS2 with narrowPeak settings and a threshold of FDR < 0.001, and a master peak set was generated as the union set of all called peaks across every sample analyzed (224,906 unique regions total).
Count matrices were made using featureCounts and DEseq2 v1 was used for differential accessibility analysis.
Annotation of genomic regions was performed using ChIPSeeker, interactive visualization of processed data was done using Degust and Rstudio along with ggplot2 and tidyverse plugins were used to generate data visualizations.
Sequencing-depth normalized ATAC bigWig files were generated using deeptools bamCoverage v3.0.1.
Assembly: hg38
Supplementary files format and content: narrowPeak files containing peak calls for each sample.
Supplementary files format and content: bigwig signal profiles for each sample, normalized by library size

molecule: genomic DNA

source_name: HFF

growth_protocol: Primary human neonatal fibroblasts (HFF cells) were acquired from ATCC (CRL-2097) and cultured in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic. A549 cells were cultured in F-12K Medium from ATCC (30-2004) with 10% FBS. All work was performed within 30 doublings from the initial passage of the vial.

extract_protocol:
Omni-ATAC-seq protocol was used to minimize mitochondrial reads from the preps, however no trypsinization was used and instead on-plate disruption/removal of nuclei (using the digitonin present in the lysis buffer) was used to better preserve nuclear mechanical context and connectivity prior to transposition by the Tn5.
The Omni-ATAC-seq protocol was used to minimize mitochondrial reads from the preps, however no trypsinization was used and instead on-plate disruption/removal of nuclei (using the digitonin present in the lysis buffer) was used to better preserve nuclear mechanical context and connectivity prior to transposition by the Tn5.  Following the final PCR, libraries were cleaned with a 0.5x/1.8x double-sided SPRI clean. Libraries were subjected to quality control by determining the number of cycles required to reach 25% of the peak threshold in the diagnostic PCR, as well as running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration. Libraries were individually diluted to 6nM and then pooled at equal volumes prior to sequencing on an Illumina HiSeq 4000 using a single lane of 50bp single end reads.

treatment_protocol: HFFs were seeded on 35mm Matrigen dishes of varying stiffness (1, 12, 50 kPa elastic modulus) coated with 10ug/mL fibronectin. HFFS were seeded at slightly variable densities to account for reduced cell attachment on softer substrates (70k, 45k, 40k HFF cells seeded per group) and allowed to culture for 20 hours. A549s were seeded in a similar fashion with Matrigen T75 flasks (1, 50 kPa elastic modulus) seeded with either 2 million and 1.25 million cells per flask, respectively and allowed to culture for 20 hours. For Y-27632 ROCKi experiments, the cells were seeded as normal, but 1 hour prior to harvest 10 μM Y-27632 ROCKi (StemCell Tech) in growth media was added to the cells. For verteporfin (Sigma-Aldrich) and CCG-222740 (MedChemExpress) studies, these inhibitors were added 18 hr prior to harvest and used at 0.7 μM and 20 μM, respectively.

value: HFF

value: Human foreskin fibroblasts

value: 1kPa surface + 0.7 μM verteporfin (18h)


title: Yeast, PolysomeProf, R1, 30C, NonDepl, Pool3

description: Library name: GFB.15062_PolyProfNonDepl30rep1tri_S15


title: Yeast, PolysomeProf, R1, 30C, NonDepl, Pool2

description: Library name: GFB.15061_PolyProfNonDepl30rep1di_S14


title: Wildtype 1

description: Library name: Sample 1


title: PRO-SEQ of shRFC3 cells rep1

description: Library name: shRFC3_1


title: Yeast, PolysomeProf, R1, 30C, NonDepl, Pool1

description: Library name: GFB.15060_PolyProfNonDepl30rep1mono_S13


title: Yeast, PolysomeProf, R3, 30C, NonDepl, Pool3

description: Library name: GFB.15058_PolyProfNonDepl30rep3tri_S11


title: Yeast, PolysomeProf, R3, 30C, NonDepl, Pool4

description: Library name: GFB.15059_PolyProfNonDepl30rep34_S12


title: PRO-SEQ of shCtrl cells rep2

description: Library name: shCtrl_2


title: batch1, WT tumor, anti-PD-1 treated, replicate 1

city: Houston

first: Jielin

last: Liu

state: TX

address: 7455 Fannin St

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

description:
Library name: C_PD1_1
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The NextSeq RTA was used for base calling
bcl2fastq was used to convert the .bcl files into .fastq files
Sequencing data were processed using the Cell Ranger software from 10X Genomics to obtain raw read counts
read counts from samples were aggregated using Cell Ranger software
Assembly: mm10
Supplementary files format and content: tsv and mtx fromat, raw counts

source_name: tumor

extract_protocol:
Single cell RNA sequencing library was generated using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit
Reverse transcription, cDNA amplification and sample indexing were performed to generate barcoded single cell libraries

value: tumor

value: all cell

value: WT

tag: batch


title: batch1, WT tumor, anti-PD-1 treated, replicate 2

description:
Library name: C_PD1_2
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz


title: PRO-SEQ of shCtrl cells rep1

description: Library name: shCtrl_1


title: Yeast, PolysomeProf, R3, 30C, NonDepl, Pool1

description: Library name: GFB.15056_PolyProfNonDepl30rep3mono_S9


title: Yeast, PolysomeProf, R3, 30C, NonDepl, Pool2

description: Library name: GFB.15057_PolyProfNonDepl30rep3di_S10


title: Yeast, PolysomeProf, R2, 30C, NonDepl, Pool4

description: Library name: GFB.15055_PolyProfNonDepl30rep24_S8


title: Fibroblasts, si-CTL, A1

description: Library name: Sample 1

value: Keloid Fibroblasts

value: wild type


title: PRO-SEQ of BRIP1 OE cells rep2

description: Library name: BRIP1_2


title: PRO-SEQ of BRIP1 OE cells rep1

description: Library name: BRIP1_1


title: batch1, WT tumor, PBS treated, replicate 2

description:
Library name: C_PBS_2
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz

value: PBS


title: Yeast, PolysomeProf, R2, 30C, NonDepl, Pool2

description: Library name: GFB.15053_PolyProfNonDepl30rep2di_S6


title: Yeast, PolysomeProf, R2, 30C, NonDepl, Pool1

description: Library name: GFB.15052_PolyProfNonDepl30rep2mono_S5


title: Yeast, PolysomeProf, R1, 42C, NonDepl, Pool4

description: Library name: GFB.15051_PolyProfNonDepl42rep14_S4


title: Wildtype 2

description: Library name: Sample 2

value: Frontal cortex


title: batch1, Ptdss1 KD tumor, anti-PD-1 treated, replicate 2

description:
Library name: K_PD1_2
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz

value: Ptdss1 KD


title: Yeast, PolysomeProf, R1, 42C, NonDepl, Pool3

description: Library name: GFB.15050_PolyProfNonDepl42rep1tri_S3


title: Yeast, PolysomeProf, R2, 30C, NonDepl, Pool3

description: Library name: GFB.15054_PolyProfNonDepl30rep2tri_S7


title: batch1, WT tumor, PBS treated, replicate 1

description:
Library name: C_PBS_1
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz


city: Boston

first: Dan

last: Barouch

state: MA

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

description: Library name: p22286_s024_J639_Male_20_21_Group_2_D0_Post_ATI_BatchB

data_processing:
The quality of the raw reads was assessed using multiQC39. Raw demultiplexed fastq paired-end read files were trimmed of adapters and filtered using the program skewer to discard those with an average phred quality score of less than 30 or a length of less than 36.
Data were aligned to the Mmul10-100 assembly and annotations of the Indian rhesus macaque genome using STAR version 2.7.3a.
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
Assembly: Mmul10-100
Supplementary files format and content: siv-reservoir-biomarkers-rawCounts.csv (raw RNA sequencing counts)
Supplementary files format and content: siv-reservoir-biomarkers-normalizedCounts.csv (normalized RNA sequencing counts)

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood samples using the PAXgene Blood RNA Kit IVD (PreAnalytix).
RNA quality was assessed with the Fragment Analyzer (Agilent) and its Standard Sensitivity RNA kit. Total RNA was normalized to 100 ng before random hexamer priming and libraries were generated by the TruSeq Stranded Total RNA—Globin kit (Illumina). The resulting libraries were assessed on the Fragment Analyzer (Agilent) with the High Sense Large Fragment kit and quantified using a Qubit 3.0 fluorometer (Life Technologies). Medium-depth sequencing, with at least 30 million reads per sample, was performed on a NextSeq 500 (Illumina) with a PE100 configuration, paired-end run yielding ~40 million reads per sample.

value: Whole blood

tag: animal id

tag: Sex

value: Male

value: BatchB

tag: viral loads_(cp/ml)


title: Yeast, PolysomeProf, R1, 42C, NonDepl, Pool2

description: Library name: GFB.15049_PolyProfNonDepl42rep1di_S2


title: PRO-SEQ of DHX36 OE cells rep1

description: Library name: DHX36_1

value: liver


title: batch1, Ptdss1 KD tumor, anti-PD-1 treated, replicate 1

description:
Library name: K_PD1_1
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz


title: batch1, Ptdss1 KD tumor, PBS treated, replicate 2

description:
Library name: K_PBS_2
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz


title: PRO-SEQ of Ctrl cells rep1

description: Library name: Ctrl_1

value: tumor cells


title: Yeast, PolysomeProf, R1, 42C, NonDepl, Pool1

description: Library name: GFB.15048_PolyProfNonDepl42rep1mono_S1


title: batch1, Ptdss1 KD tumor, PBS treated, replicate 1

description:
Library name: K_PBS_1
10X Genomics
r1_barcodes.tsv.gz, r1_features.tsv.gz, r1_matrix.mtx.gz


title: Thymus, Trp53+/+_mouse_1611, 4.5_month-old

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description: Microwell-based ATAC-seq

library_source: genomic single cell

data_processing:
The original FASTQ files were converted to BAM format firstly. Then the cell barcodes were extracted and tagged with CB in the offered BAM files. Three 6bp barcodes and one 10bp Tn5 barcode ware combined to identify a single cell (a single cell barcode consists of four barcode fragments). Reads with the quality of cell barcodes less than 10 were tagged with XQ and removed afterwards. The processing above was based on Drop-seq_tools-2.5.1. Next, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each barcode fragments. Before alignment, the cell barcodes were added to the query names, the BAM files were converted to the FASTQ files and the 28bp barcodes at the 5’ end were trimmed simultaneously.
BWA (version 0.7.15), which is encapsulated in Snaptools, was used for reads alignment in single-end mode. The data were aligned to mm10 reference genome. Snaptools was again used to convert the aligned and shifted BAM files to SNAP files, which was then converted to Fragment files (BED format). The sorted and compressed Fragment files in BED format were required as inputs for subsequent analysis.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

source_name: Thymus

extract_protocol:
Tissues were quickly transferred into cold DPBS, then washed and subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into pre-labelled and pre-chilled 1.5 ml nuclease-free tubes. After that, the powder in each tube was suspended in 1 ml Nuclear Permeabilization Buffer [1 × DPBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1 × Protease inhibitor], and followed by incubation for 3 minutes to isolate the nuclei. The suspension was transferred to a 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, filtered through 40 μm strainers and centrifuged at 600 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.  For Bone marrow, cells were collected and centrifuged at 300 × g for 5 minutes at 4°C, then suspended in 1 ml Nuclear Permeabilization Buffer and followed by incubation for 6 minutes to isolate the nuclei. The suspension was transferred to 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, centrifuged at 500 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.
Library preparations were performed with the Microwell ATAC-seq plus protocol

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 ml PBS.

value: Thymus

tag: strain

tag: age

value: 4.5 months

value: Female


title: Stomach, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Stomach

value: Stomach


title: RU779_SCLC_MET_LI_sn

city: New York

first: Karan

last: Luthria

state: New York

address: 650 W 168th Street

department: Medicine

institute: Columbia University Vagelos College of Physicians and Surgeons

description:
Library name: RU779_MET_LI
Single nuclei RNA sequencing

data_processing:
Raw snRNA-seq data were analyzed using Cell Ranger (v6.1.1). Transcripts were aligned to the human GRCh38 reference genome.
Ambient RNA was removed using CellBender (v0.2.0). Gene expression matrices were processed individually in R (v4.1.1) using Seurat (v4.1.0).
Filters were applied to keep cells with 500–10,000 genes, 1,000–60,000 UMIs, and <10% of mitochondrial reads in each individual sample.
Scrublet v0.2.1 (Wolock et al., 2019) was applied to identify and remove doublets with an expected doublet rate ranging from 2.5–7.5% based on the loading rate.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix

molecule: nuclear RNA

source_name: liver metastasis

extract_protocol:
Single-nuclei suspension from frozen SCLC primary and metasasis were generated using methods published in Slyper et al. (Nature Medicine, 2020) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST)  followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 15,000 nuclei were separated for droplet-based RNA capture and reverse transcription using 10x Genomics  5' v1.1 or 5' v2.0 reagents and a Chromium controller.
Single-nuclei RNAseq (snRNA-seq) libraries were generated using Chromium 5' (V1.1 and V2) reagents according to the manufacturer protocol with one additional cycle during library amplification to account for lower material input from nuclei compared to whole cells.

value: liver metastasis

value: tumor cell (nuclei)

tag: tumor state

value: metastasis

tag: disease type

value: small cell lung cancer

value: Chan Cohort


title: WT tumor, anti-PD-1 treated, replicate 4

description:
Library name: WT_PD1_4
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: tumor

tag: cell type

value: CD45+ cell

tag: genotype

value: WT


title: Spleen, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Spleen

tag: tissue

value: Spleen


title: SmallIntestine, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: SmallIntestine

value: SmallIntestine


title: PRO-SEQ of Ctrl cells rep2

description: Library name: Ctrl_2

tag: treatment

value: Early S Phase-Synchronized


title: WT tumor, anti-PD-1 treated, replicate 2

description:
Library name: WT_PD1_2
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: RU426_SCLC_PRI_LU_sn

description:
Library name: RU426_PRI_LU
Single nuclei RNA sequencing

source_name: lung tumor

value: lung tumor

value: primary


title: Pancreas, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Pancreas

value: Pancreas


title: Lung, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Lung

value: Lung

value: 4.5 months


title: MammaryGland, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: MammaryGland

value: MammaryGland

value: Female


title: Uterus, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Uterus

value: Uterus


title: WT tumor, anti-PD-1 treated, replicate 1

description:
Library name: WT_PD1_1
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: RU1322_SCLC_MET_LN_sn

description:
Library name: RU1322_MET_LN
Single nuclei RNA sequencing

source_name: lymph node metastasis

value: lymph node metastasis

value: tumor cell (nuclei)

value: metastasis


title: LymphNodes, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: LymphNodes

value: LymphNodes


title: LargeIntestine, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: LargeIntestine

value: LargeIntestine


title: PRO-SEQ of DHX36 OE cells rep2

description: Library name: DHX36_2

source_name: liver

value: liver

value: tumor cells


title: Kidney, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Kidney

value: Kidney


title: WT tumor, anti-PD-1 treated, replicate 3

description:
Library name: WT_PD1_3
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: tumor

value: tumor

value: CD45+ cell

value: WT


title: Liver, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Liver

value: Liver


title: WT tumor, PBS treated, replicate 4

description:
Library name: WT_PBS_4
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: PBS


title: RU1311_SCLC_REC_LU_sn

description:
Library name: RU1311_REC_LU
Single nuclei RNA sequencing

value: lung tumor

value: recurrance

value: small cell lung cancer

value: Chan Cohort


title: RU1231A_SCLC_MET_LN_sn

description:
Library name: RU1231A_MET_LN
Single nuclei RNA sequencing

value: lymph node metastasis


title: Ovary, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Ovary

value: Ovary

value: 4.5 months

value: Female


title: WT tumor, PBS treated, replicate 3

description:
Library name: WT_PBS_3
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: RU1229A_SCLC_PRI_LU_sn

description:
Library name: RU1229A_PRI_LU
Single nuclei RNA sequencing

value: tumor cell (nuclei)

value: primary


title: WT tumor, PBS treated, replicate 2

description:
Library name: WT_PBS_2
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: Thymus, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Thymus

value: Thymus

value: 6 months

value: Male


title: Stomach, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Stomach

value: Stomach


title: Spleen, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Spleen

value: Spleen


title: RU1195A_SCLC_REC_LU_sn

description:
Library name: RU1195A_REC_LU
Single nuclei RNA sequencing


title: WT tumor, PBS treated, replicate 1

description:
Library name: WT_PBS_1
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: tumor

value: CD45+ cell

value: WT


title: Ptdss1 KD tumor, anti-PD-1 treated, replicate 4

description:
Library name: KD_PD1_4
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: Ptdss1 KD


title: RU1293A_SCLC_MET_LN_sn

description:
Library name: RU1293A_MET_LN
Single nuclei RNA sequencing

value: metastasis

value: small cell lung cancer


title: Ptdss1 KD tumor, anti-PD-1 treated, replicate 3

description:
Library name: KD_PD1_3
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: Heart, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Heart

value: Heart


title: RU1181_SCLC_MET_LN_sn

description:
Library name: RU1181_MET_LN
Single nuclei RNA sequencing

value: lymph node metastasis

value: Chan Cohort


title: 30 waf, Sample C

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

description: Library name: DecC

data_processing:
The Sequencing was performed in a DNBSEQ G400 platform, BGI (Beijing Genomics Institute, Shenzhen, China).
Raw sequencing data were filtered using SOAPnuke software (version 1.5.2) to exclude low quality reads
Clean reads were mapped onto the Olea europaea reference genome (GCF_002742605.1), by means of HISAT2 software (version 2.0.4). Novel gene prediction was performed using StringTie (version 1.0.4) to reconstruct transcripts, Cuffcompare (version 2.2.1) to compare them to reference annotation and CPC (version 0.9-r2) to predict coding potential of the novel transcripts. Novel coding transcripts were merged with reference transcripts to get the complete reference, and the clean reads were mapped using Bowtie2 (version 2.2.5).
Gene expression level was calculated with RSEM with default parameters.
Normalization in fragments per kilobase per million mapped fragments FPKM)
Assembly: O_europaea_v1 (GCF_002742605.1)
Supplementary files format and content: Text file with  FPKM values of the trascripts of 17, 21, 26 and 30 waf

organism: Olea europaea

source_name: fruit mesocarp

growth_protocol: The fruit samples were collected during the 2019 growing season. The olive trees (Olea europea L., cultivar “Koroneiki”) were planted in a field, located on a hilly area near the location of ancient Olympia in Western Greece (40°48′43’’ N, 23°59′25’’ E, at an altitude of 330 m). Irrigation, fertilization, pest and canopy management were applied according to standard local agronomical practices. Samples were collected at four time points during fruit maturation, specifiacally at 17, 21, 26 and 30 Weeks After Flowering (WAF).

extract_protocol:
Total RNA was extracted from olive mesocarp samples using a modified CTAB extraction protocol (Zymo Research, Irvine, CA, USA) and the Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) with an on-column DNase treatment, according to the manufacturer’s instructions.
The RNA quality was determined by NanoDropTM and Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). Afterwards, the cDNA libraries were constructed and sequenced in DNBseq platform (BGI, Hong Kong).

value: fruit mesocarp

value: 30 waf


title: Pancreas, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Pancreas

value: Pancreas


title: 30 waf, Sample B

description: Library name: DecB


title: SmallIntestine, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: SmallIntestine

value: SmallIntestine


title: SalivaryGland, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: SalivaryGland

value: SalivaryGland

value: 6 months


title: LymphNodes, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

value: LymphNodes

value: Male


title: 26 waf, Sample C

description: Library name: NovC

value: 26 waf


title: BoneMarrow, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: BoneMarrow

value: BoneMarrow

value: 4.5 months

value: Female


title: RU1181_SCLC_PRI_LU_sn

description:
Library name: RU1181_PRI_LU
Single nuclei RNA sequencing

source_name: lung tumor

value: lung tumor

value: tumor cell (nuclei)

value: primary


title: Ptdss1 KD tumor, anti-PD-1 treated, replicate 2

description:
Library name: KD_PD1_2
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: tumor

value: CD45+ cell

value: Ptdss1 KD


title: 30 waf, Sample A

description: Library name: DecA

value: fruit mesocarp

value: 30 waf


title: RU1152_SCLC_MET_LN_sn

description:
Library name: RU1152_MET_LN
Single nuclei RNA sequencing

source_name: lymph node metastasis

value: lymph node metastasis

value: metastasis

value: small cell lung cancer

value: Chan Cohort


title: Bladder, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Bladder

value: Bladder


title: Brain, Trp53+/+_mouse_1611, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Brain

value: Brain


title: RU1144_SCLC_REC_LU_sn

description:
Library name: RU1144_REC_LU
Single nuclei RNA sequencing

value: recurrance


title: RU1215_SCLC_MET_PL_sn

description:
Library name: RU1215_MET_PL
Single nuclei RNA sequencing

source_name: pleural metastasis

value: pleural metastasis


title: Ptdss1 KD tumor, anti-PD-1 treated, replicate 1

description:
Library name: KD_PD1_1
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: tumor


title: Ptdss1 KD tumor, PBS treated, replicate 4

description:
Library name: KD_PBS_4
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: PBS


title: RU1144_SCLC_MET_LM_sn

description:
Library name: RU1144_MET_LN
Single nuclei RNA sequencing


title: RU1108a_SCLC_REC_LU_rpmi_sn

description:
Library name: RU1108a_REC_LU_rpmi
Single nuclei RNA sequencing

value: lung tumor


title: Liver, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Liver

value: Liver

value: 6 months

value: Male


title: 26 waf, Sample A

description: Library name: NovA

value: 26 waf


title: LargeIntestine, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: LargeIntestine

value: LargeIntestine


title: RU1108a_SCLC_REC_LU_bf_sn

description:
Library name: RU1108a_REC_LU_bf
Single nuclei RNA sequencing

value: tumor cell (nuclei)


title: 21 waf, Sample C

description: Library name: OctC

value: fruit mesocarp

value: 21 waf


title: Ptdss1 KD tumor, PBS treated, replicate 2

description:
Library name: KD_PBS_2
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: tumor

value: CD45+ cell

value: Ptdss1 KD


title: Kidney, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Kidney

value: Kidney


title: Urethra Stroma, Adult mus female, rep 2

city: Bengaluru

first: Diya

last: Binoy Joseph

state: Karnataka

address: GKVK - Post, Bellary Rd

country: India

institute: Institute for Stem Cell Science and Regenerative Medicine

description:
Library name: URSt_2
10x Genomics 3' gene expression

data_processing:
Base calling: Illumina bcl2fastq
Barcoding processing and single cell 3' counting: cellranger-8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes)
Assembly: GRCm39
Supplementary files format and content: filtered feature-barcode matrix, .h5 files

molecule: polyA RNA

source_name: Urethral Stroma

growth_protocol: CD-1 wildtype female mice at 7-9 weeks were used for this study

extract_protocol:
Whole urethras were dissected and washed with HBSS to remove fat and debris. Cells were chopped and digested in Accutase supplemented with DNaseI and 10 uM Rock inhibitor Y-27632 for 1.5 hours. Cells were triturated to generated single suspensions and passed through a 30 micron filter to obtain single cells. Following RBC lysis, cell counts were obtained using a hemocytometer. Single cells were loaded onto the Chromium controller for single cell partitioning and barcoding. For single cell isolation of the epithelial and stromal compartments, female urethras were cut into two pieces each digested in a 1% trypsin solution containing DNaseI. Epithelial tissue was mechanically separated from the stromal tissue. Tissues were separately digested to single cells using Accutase as described above for the whole urethras.
A target of 10,000 cells per sample was loaded on to the 10x Chromium contoller for cell partitioning. Libraries were prepared according to the manufacturers instructions for the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1. Briefly, cells were resuspended in the master mix and loaded along with the partitioning oil and gel beads onto the Chromium Next GeM Chip G to generate gel bead-in emulsions (GEM). Poly-A mRNAs captured by the beads were reverse transcribed to cDNA along with the unique molecular identified (UMI), Illumina R1 primer and the cell barcode. Following reverse transcriptions, GEMs were broken up and cDNAs were pooled. Silane magnetic beads were used to purify first strand cDNA from the RT mixture. Full length cDNA was amplified by PCR. Enzymatic fragmentation and size selection was performed to obtain desired read lengths. Illumina R2 primer, P5 and P7 bridge amplification primers and sample index is introduced using end-repair, A-tailing, ligation and PCR. Librariers were pooled for sequencing.

treatment_protocol: No treatment was applied

value: Urethral Stroma

value: Female

value: 7-9 weeks

value: Wildtype


title: Urethra Stroma, Adult mus female, rep 1

description:
Library name: URSt_1
10x Genomics 3' gene expression


title: Heart, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

value: Heart


title: 21 waf, Sample B

description: Library name: OctB


title: RU1108a_SCLC_REC_LU_b_sn

description:
Library name: RU1108a_REC_LU_b
Single nuclei RNA sequencing

value: lung tumor

value: recurrance

value: small cell lung cancer

value: Chan Cohort


title: RU1080_SCLC_MET_KID_sn

description:
Library name: RU1080_MET_KID
Single nuclei RNA sequencing

source_name: kidney metastasis

value: kidney metastasis

value: metastasis


title: Gallbladder-BileDuct, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Gallbladder-BileDuct

value: Gallbladder-BileDuct

value: 6 months

value: Male


title: Urethra Epithelium, Adult mus female, rep 2

description:
Library name: UREpi_2
10x Genomics 3' gene expression

source_name: Urethral Epithelium

value: Urethral Epithelium


title: 17 waf, Sample C

description: Library name: SepC

source_name: fruit mesocarp

value: fruit mesocarp

value: 17 waf


title: RU1066_SCLC_PRI_LU_sn

description:
Library name: RU1066_PRI_LU
Single nuclei RNA sequencing

value: tumor cell (nuclei)

value: primary


title: Brain, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

value: Brain


title: Urethra Epithelium, Adult mus female, rep 1

description:
Library name: UREpi_1
10x Genomics 3' gene expression

value: Female

value: 7-9 weeks

value: Wildtype


title: RU1065C_SCLC_MET_LI_sn

description:
Library name: RU1065C_MET_LI
Single nuclei RNA sequencing

source_name: liver metastasis

value: liver metastasis


title: Ptdss1 KD tumor, PBS treated, replicate 3

description:
Library name: KD_PBS_3
10X Genomics
barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: tumor

value: CD45+ cell

value: Ptdss1 KD

value: PBS


title: Urethra, Adult mus female, rep 2

description:
Library name: UR_2
10x Genomics 3' gene expression

source_name: Urethra

value: Urethra


title: 26 waf, Sample B

description: Library name: NovB

value: 26 waf


description: Library name: p22286_s026_J639_Male_20_21_Group_2_D8_Post_ATI

source_name: Whole blood

value: Whole blood

value: Male

value: BatchA


title: 17 waf, Sample A

description: Library name: SepA

value: fruit mesocarp

value: 17 waf


title: sclc_pa151_3p_sn

description:
Library name: pa151_3p
Single nuclei RNA sequencing

source_name: brain metastasis

value: brain metastasis

value: tumor cell (nuclei)

value: metastasis

value: small cell lung cancer

value: CUIMC Cohort


title: sclc_pa168_3p_sn

description:
Library name: pa168_3p
Single nuclei RNA sequencing


title: Stomach, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Stomach

value: Stomach

value: 4.5 months

value: Female


title: Bladder, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Bladder

value: Bladder

value: 6 months


title: Urethra, Adult mus female, rep 1

description:
Library name: UR_1
10x Genomics 3' gene expression

value: Urethra

value: 7-9 weeks

value: Wildtype


title: 21 waf, Sample A

description: Library name: OctA

value: 21 waf


title: mouse neutrophil, 36h no-larvae imm, 05

city: Philadelphia

first: Nathan

middle: M

last: Ryan

institute: Thomas Jefferson University

description:
Library name: 48_36h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

data_processing:
Using a Linux computing cluster, sequencing reads were trimmed to remove low-quality or adapter-containing sequences using Trimmomatic v. 0.39, with the following settings LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were mapped to the NCBI mm10 Mus musculus reference genome using STAR. Mapped reads were quantified using HTseq-count, with the following settings --mode union -a 1.
Mapped read count data were further analyzed in R, as follows: Counts were filtered to retain genes with count values greater than 0 for six or more samples, normalized and scaled to obtain counts per million (CPM) values using edgeR
Differentially expressed genes between immunized versus control groups were identified within each time point (18 hours or 36 hours), for diffusion chambers with or without larvae, using DESeq2
For each grouping (i.e., 18 h with larvae, 18 h without larvae, 36 h with larvae, 36 h without larvae), a DESeq2 model was fit using ~immunization as the model design parameter.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (RNAseq_data-analyzed.xlsx) contains gene ID, mean read counts, log2FoldChange between control and immune mice, individual and FDR-adjusted p values, individual read counts for each sample, gene name, description, GO accession numbers and descriptions. The file is divided into 4 sheets based on time point and whether larvae were present in the diffusion chambers from which the neutrophils were collected.

source_name: Subcutaneous

extract_protocol:
The total RNA was isolated using the Qiagen RNAeasy Plus kit. RNA concentration was quantified using a Qubit fluorimeter, and integrity was determined by the TapeStation high-sensitivity RNA kit (Agilent Technologies, Santa Clara, CA, USA).
mRNA libraries were prepared by poly-A selection from 1 ng of each sample using the Takara SMART-seq HT kit (Takara, 634437).

treatment_protocol: Mice were either immunized with recombinant fusion protein vaccine plus adjuvant or adjuvant only controls

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: WT

value: Male

value: BALB/cByJ

value: Imm

tag: time

value: 36 hr


title: 17 waf, Sample B

description: Library name: SepB

value: fruit mesocarp

value: 17 waf


title: SmallIntestine, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: SmallIntestine

value: SmallIntestine

value: 4.5 months

value: Female


title: mouse neutrophil, 36h no-larvae ctrl, 06

description:
Library name: 47_36h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Ctrl


title: sclc_pa146_3p_sn

description:
Library name: pa146_3p
Single nuclei RNA sequencing

value: brain metastasis

value: tumor cell (nuclei)

value: metastasis

value: small cell lung cancer

value: CUIMC Cohort


title: Atg5-KO LPS injected retina

city: St. Louis

first: Philip

last: Ruzycki

state: MO

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

description:
Library name: Atg5-KO
10X Genomics

data_processing:
Resulting libraries were sequenced on an Illumina NovaSeq 6000 at the McDonnell Genome Institute at Washington University School of Medicine. Raw fastq files were processed using CellRanger (v6.0.0) and mapped to the mouse genome (mm10). Further analysis was performed using Seurat (v5.2.1) in R. The full code for this analysis is available at https://github.com/p-ruzycki/Atg5KO_LPS.
Assembly: mm10
Supplementary files format and content: ko_barcodes.tsv.gz: list of cell barcodes from Atg5-KO sample
Supplementary files format and content: wt_barcodes.tsv.gz: list of cell barcodes from Control sample
Supplementary files format and content: ko_matrix.mtx.gz: sparse matrix of UMI counts from Atg5-KO sample
Supplementary files format and content: wt_matrix.mtx.gz: sparse matrix of UMI counts from Control sample
Supplementary files format and content: features.tsv.gz: list of gene identifiers

source_name: retina

extract_protocol:
Single cell suspensions were generated from pooled isolated retinas for each group (n=6) with a Papain Dissociation kit using the protocol provided. The final cell pellet was resuspended in PBS (pH7.4) with 0.1% BSA and cell viability assessed using Trypan blue staining. Only samples with >85% viability were used.
Single-cell RNA sequencing (scRNA-seq) was performed using the 10X Genomics platform and reagents (3’v3.1) according to the manufacturer’s instructions

treatment_protocol: LPS (0.5 µg/eye) was delivered to the vitreous cavity in PBS.

value: retina

value: GLAST-CreER; Atg5fl/fl

value: 0.5 ug/eye LPS, 4-hydroxy-tamoxifen


title: Spleen, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Spleen

value: Spleen


title: BoneMarrow, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: BoneMarrow

value: BoneMarrow

value: 6 months

value: Male


title: mouse neutrophil, 36h no-larvae ctrl, 05

description:
Library name: 46_36h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: WT

value: BALB/cByJ

value: 36 hr


title: Lung, Trp53+/+_mouse_1602, 6_month-old

description: Microwell-based ATAC-seq

source_name: Lung

value: Lung


title: mouse neutrophil, 36h larvae imm, 07

description:
Library name: 45_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Imm


title: Ovary, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Ovary

value: Ovary

value: 4.5 months

value: Female


title: Pancreas, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Pancreas

value: Pancreas


title: Mouse hippocampus from aging animals treated with iMPs, rep 4

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: 10x Genomics

data_processing:
Sample demultiplexing was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core.  Raw data were delivered as multiple gzipped fastq files.
Demultiplexed fastq files were run via CellRanger v6.1.2 using the "cellranger count" command with the "--include-introns" option using the 10x-provided mouse reference sequence v2020-A.
Cellranger output filtered_feature_bc_matrix.h5 files were used for subsequent analysis
Assembly: mm10
Supplementary files format and content: Cellranger output filtered_feature_bc_matrix.h5 files

source_name: Brain, Hippocampus

extract_protocol:
All steps were performed on ice.  Wide-bore Rainin LTS pipette tips were used exclusively throughout. Frozen mouse hippocampus tissue was thawed on ice, resuspended in cold homogenization buffer (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, 320 mM Sucrose, 0.1 mM EDTA, 0.1% NP40, RNAse inhibitors, and Protease inhibitors), and transferred to a 2 ml glass dounce.  The tissue was manually lysed with 50 strokes each of the "A" and "B" pestles.  Homogenate was filtered using 70 um Flowmi pipette tip filters and gently mixed 1:1 with a 50% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, and 50% Iodixanol).  A centrifugation gradient was set up using 600 ul 40% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, 0.2 ug/ul OrangeG, and 40% Iodixanol), 600 ul 29% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, and 29% Iodixanol) and 800 ul of the 50% Iodixanol + Sample mixture (25% Iodixanol final concentration).  This was centrifuged at 3000 x g for 1 hour with the breaks disengaged.  Any debris on the top surface was removed, and 200 ul of the thin cloudy layer containing the nuclei was extracted, mixed with 1.8 ml PBS + 1% BSA solution, and centrifuged at 500 x g for 10 minutes with breaks engaged.  1.8 ml supernatant was removed and the remaining 200 ul plus nuclei pellet was resuspended in 1.8 ml PBS + 1% BSA solution.  The nuclei suspension was counted via hemocytometer and checked for nucleus quality.  A portion of this suspension was then diluted to achieve the correct nuclei concentration for the 10x Chromium NextGEM 3' protocol with a target of ~4,000 nuclei per sample.
Standard 10x protocol found in "Chromium NextGEM Single Cell 3' Reagent Kits v3.1 User Guide, Rev D" (single index)

value: Brain, Hippocampus

value: NOD scid gamma

value: iMPs


title: Mouse hippocampus from aging animals treated with iMPs, rep 5

description: 10x Genomics


title: mouse neutrophil, 36h no-larvae ctrl, 04

description:
Library name: 44_36h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Ctrl


title: sclc_pa124_3p_sn

description:
Library name: pa124_3p
Single nuclei RNA sequencing

value: brain metastasis

value: tumor cell (nuclei)

value: metastasis

value: small cell lung cancer

value: CUIMC Cohort


title: sclc_pa124_5pv2_sn

description:
Library name: pa124_5pv2
Single nuclei RNA sequencing


title: mouse neutrophil, 36h no-larvae imm, 04

description:
Library name: 43_36h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: WT

value: Male

value: BALB/cByJ


title: MammaryGland, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: MammaryGland

value: MammaryGland

value: 4.5 months

value: Female


title: Mouse hippocampus from aging animals treated with iMPs, rep 3

description: 10x Genomics

value: Brain, Hippocampus

value: NOD scid gamma


title: Control LPS injected retina

description:
Library name: Control
10X Genomics

value: retina

value: 0.5 ug/eye LPS


title: sclc_pa150_3p_sn

description:
Library name: pa150_3p
Single nuclei RNA sequencing

value: brain metastasis

value: tumor cell (nuclei)


title: LargeIntestine, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: LargeIntestine

value: LargeIntestine


title: sclc_pa098_3p_sn

description:
Library name: pa098_3p
Single nuclei RNA sequencing

value: metastasis

value: small cell lung cancer

value: CUIMC Cohort


title: mouse neutrophil, 36h no-larvae imm, 03

description:
Library name: 42_36h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: Imm

value: 36 hr


title: sclc_pa096_3p_sn

description:
Library name: pa096_3p
Single nuclei RNA sequencing


title: sclc_pa031_5pv2_sn

description:
Library name: pa031_5pv2
Single nuclei RNA sequencing


title: Kidney, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Kidney

value: Kidney

value: 4.5 months


title: Mouse hippocampus from aging animals treated with iMPs, rep 1

description: 10x Genomics

value: Brain, Hippocampus

value: iMPs


title: sclc_pa013_5pv2_sn

description:
Library name: pa013_5pv2
Single nuclei RNA sequencing


title: mouse neutrophil, 36h no-larvae ctrl, 03

description:
Library name: 41_36h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: WT

value: Male

value: BALB/cByJ

value: Ctrl


title: mouse neutrophil, 36h no-larvae ctrl, 02

description:
Library name: 40_36h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description


title: Ptdss1 KD tumor, PBS treated, replicate 1

description:
Library name: KD_PBS_1
10X Genomics

source_name: tumor

value: tumor

value: CD45+ cell

value: Ptdss1 KD

value: PBS


title: Mouse hippocampus from aging animals treated with iMPs, rep 2

description: 10x Genomics

value: NOD scid gamma


title: Gallbladder-BileDuct, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Gallbladder-BileDuct

value: Gallbladder-BileDuct

value: Female


title: Mouse hippocampus from aging animals treated with vehicle, rep 5

description: 10x Genomics

value: vehicle


title: sclc_ns007_3p_sn

description:
Library name: ns007_3p
Single nuclei RNA sequencing

source_name: brain metastasis

value: brain metastasis

value: tumor cell (nuclei)

value: metastasis

value: small cell lung cancer

value: CUIMC Cohort


title: Mouse hippocampus from aging animals treated with vehicle, rep 4

description: 10x Genomics

value: Brain, Hippocampus


title: mouse neutrophil, 36h no-larvae imm, 01

description:
Library name: 38_36h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: WT

value: Male

value: Imm

value: 36 hr


title: BoneMarrow, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

value: BoneMarrow

value: 4.5 months


title: sclc_n3657_3p_sn

description:
Library name: n3657_3p
Single nuclei RNA sequencing


title: sclc_ns005_3p_sn

description:
Library name: ns005_3p
Single nuclei RNA sequencing


title: mouse neutrophil, 36h larvae imm, 06

description:
Library name: 36_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: BALB/cByJ


title: Mouse hippocampus from aging animals treated with vehicle, rep 3

description: 10x Genomics

value: NOD scid gamma

value: vehicle


title: mouse neutrophil, 36h no-larvae ctrl, 01

description:
Library name: 37_36h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Ctrl


title: Mouse hippocampus from aging animals treated with vehicle, rep 1

description: 10x Genomics


title: Mouse hippocampus from aging animals treated with vehicle, rep 2

description: 10x Genomics


title: Heart, Trp53+/+_mouse_0101, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Heart

value: Heart

value: Female


title: sclc_n3626_3p_sn

description:
Library name: n3626_3p
Single nuclei RNA sequencing

value: brain metastasis

value: tumor cell (nuclei)

value: metastasis

value: small cell lung cancer

value: CUIMC Cohort


title: sclc_n3628_3p_sn

description:
Library name: n3628_3p
Single nuclei RNA sequencing


title: mouse neutrophil, 36h larvae imm, 05

description:
Library name: 34_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: WT


title: Tumor1, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

value: 8 months

value: Male


title: mouse neutrophil, 36h larvae ctrl, 06

description:
Library name: 35_36h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: BALB/cByJ

value: 36 hr


title: sclc_n3525_3p_sn

description:
Library name: n3525_3p
Single nuclei RNA sequencing


title: mouse neutrophil, 36h no-larvae imm, 02

description:
Library name: 39_36h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Imm


title: Stomach, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: Stomach

value: Stomach


title: Spleen, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

value: Spleen


title: mouse neutrophil, 36h larvae ctrl, 05

description:
Library name: 33_36h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

source_name: Subcutaneous

value: Ctrl


title: Cabozantinib-resistant Caki-1 cells, Replicate 2 (RNA)

first: Marc

last: Machaalani

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: Caki-1 Resistant, Rep2, RNA

data_processing:
RNA sequencing was performed on two replicates each of the parental Caki-1 (CaboS) and CaboR cell lines using Illumina Novoseq at Novogene. The RNA reads were aligned to GRCh38 reference genome using STAR 59, quantified using RSEM 60 and evaluated for quality using RNA-seqQC2 61.  Differential gene expression between the CaboR and CaboS cell lines was conducted using the R package “DESeq2” (v.1.40.2) 62. Genes that were not expressed in two or more samples or had an average expression of less than 10 across all samples were filtered out before the analysis. A gene set enrichment analysis (GSEA) 63 was performed using the R package “clusterProfiler” (v.4.8.2) 64 on selected pathways from the Hallmark, KEGG, Reactome, Biocarta and WikiPathways.
Chromatin immunoprecipitation and sequencing (ChIP-seq) was performed on the cell lines for the post translational histone modifications H3K27ac and H3K4me3. Chromatin was sheared to 300 to 500bp using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight at 4 C with the following antibodies coupled with protein A and protein G beads (Invitrogen): H3K27ac and H3K4me3. Five percent of the sample was not exposed to antibody and was used as a control. The beads were then washed three times each with Low-Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 150 mM NaCl), High-Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 500 mM NaCl), and LiCl Wash Buffer (10 mM Tris pH 7.5, 250 mM LiCl, 1% NP-40, 1% Na-Doc, 1 mM EDTA) and rinsed with TE buffer (pH 8.0) once. The samples were then de-cross-linked, treated with RNase and proteinase K, and DNA was extracted (Qiagen). DNA sequencing libraries were prepared from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit (TakaraBio).
Assembly: hg19
Supplementary files format and content: ChIP: bigWig, narrowPeak (except for Input samples)
Supplementary files format and content: RNA: tab-delimited text files include raw counts

growth_protocol: Human Caki-1 renal cancer cell lines were obtained from the American Type Culture Collection (ATCC, Rockville, MD) and Caki-1 maintained in RPMI 1640 medium. Culture media were supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin antibiotics (Invitrogen, Carlsbad, CA).

extract_protocol:
Both cell lines were fixed using 1% formaldehyde (ThermoFisher) for 10 minutes at room temperature and then quenched with 125 mM Glycine.
Libraries were sequenced on an Illumina platform to generate 150-bp paired-end reads (Novogene).

treatment_protocol: Cabozantinib-resistant Caki-1 cells were generated by growing Caki-1 cells in McCoy's 5A (Modified) Medium (Gibco) supplemented with 10% fetal bovine serum (Sigma), 100 μg/mL streptomycin (Invitrogen), and 5 μM cabozantinib, with an incremental increase over 2 months until reaching 20 μM cabozantinib. Once the cells became resistant, they were cultured in the presence of 10 μM cabozantinib.

value: Kidney

value: Renal cell carcinoma


title: Mouse hippocampus from young animals treated with vehicle, rep 5

description: 10x Genomics

value: Brain, Hippocampus

value: NOD scid gamma

value: vehicle


title: mouse neutrophil, 36h larvae imm, 04

description:
Library name: 32_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous


title: Cabozantinib-resistant Caki-1 cells, Replicate 1 (RNA)

description: Library name: Caki-1 Resistant, Rep1, RNA


title: Mouse hippocampus from young animals treated with vehicle, rep 3

description: 10x Genomics


title: SalivaryGland, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: SalivaryGland

value: SalivaryGland


title: mouse neutrophil, 36h larvae ctrl, 04

description:
Library name: 31_36h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Primary cells

value: Neutrophil


title: SmallIntestine, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: SmallIntestine

value: SmallIntestine

value: 8 months


title: Wild-type Caki-1 cells, Replicate 2 (RNA)

description: Library name: Caki-1 WT, Rep2, RNA


title: Mouse hippocampus from young animals treated with vehicle, rep 4

description: 10x Genomics


title: Pancreas, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

value: Pancreas

value: Male


title: Wild-type Caki-1 cells, Replicate 1 (RNA)

description: Library name: Caki-1 WT, Rep1, RNA


title: Mouse hippocampus from young animals treated with vehicle, rep 1

description: 10x Genomics


title: mouse neutrophil, 36h larvae ctrl, 03

description:
Library name: 30_36h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: WT

value: BALB/cByJ

value: 36 hr


title: LymphNodes, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: LymphNodes

value: LymphNodes


title: C2C12 myotubes treated with ethanol (1/1000) for 24H, rep3

city: Paris

first: Carine

last: Beaupere

address: 27 rue Chaligny

department: Saint-Antoine Research Center

country: France

institute: INSERM

data_processing:
Mapping to reference genome: HISAT2 V2.0.5, default parameter
Quantification: HTSeq v0.6.1, -m union
Differential Expression Analysis: DESeq2, v1.24.0, Padj < 0.1
Assembly: mm10
Supplementary files format and content: txt file with differentially expressed genes in corticosterone treated cells versus VEH

source_name: cell line

growth_protocol: C2C12 cells were grown until reaching confluence in a complete medium containing DMEM 4.5g/L glucose 25 mM pyruvate (ThermoFisher Scientific, Montigny-le-Bretonneux, France), 10% FBS (fetal bovine serum, Dutscher, Issy-les-Moulineaux, France), glutamine and 1% penicillin/streptomycin. Cells were differentiated into myotubes whithin 7 days with a differentiation medium containing DMEM 4.5g/L glucose 25mM pyruvate, 2% horse serum, glutamine and 1%penicillin/streptomycin (Sigma–Aldrich, Saint Quentin Fallavier; France).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Plus Kit (QIAGEN, Hilden, Germany). RNA integrity (RIN) was assessed using Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA with a RIN above 9 were used to establish the sequencing libraries.
Library construction and sequencing were performed by Novogene Co., Ltd. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Differentiated myotubes were then treated for 24H with either 10-7M of Corticosterone (Sigma-Aldrich, St. Louis, MO) or 1uL/mL of ethanol 100%

value: cell line

value: myotubes

value: ethanol


title: mouse neutrophil, 36h larvae imm, 03

description:
Library name: 29_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Imm


title: C2C12 myotubes treated with ethanol (1/1000) for 24H, rep2


title: mouse neutrophil, 36h larvae imm, 02

description:
Library name: 28_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description


title: Cabozantinib-resistant Caki-1 cells, Replicate 2, H3K27ac (ChIP)

description: Library name: Caki-1 Resistant, Rep2, ChIP

value: Kidney

value: Renal cell carcinoma


title: Lung, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: Lung

value: Lung


title: Cabozantinib-resistant Caki-1 cells, Replicate 1, H3K27ac (ChIP)

description: Library name: Caki-1 Resistant, Rep1, ChIP


title: Wild-type Caki-1 cells, Replicate 2, H3K27ac (ChIP)

description: Library name: Caki-1 WT, Rep2, ChIP


title: mouse neutrophil, 36h larvae ctrl, 02

description:
Library name: 27_36h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Ctrl


title: C2C12 myotubes treated with ethanol (1/1000) for 24H, rep1


title: Liver, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: Liver

value: Liver

value: 8 months


title: mouse neutrophil, 36h larvae ctrl, 01

description:
Library name: 26_36h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Neutrophil

value: Male


title: Mouse hippocampus from young animals treated with vehicle, rep 2

description: 10x Genomics

value: Brain, Hippocampus

value: NOD scid gamma

value: vehicle


title: Kidney, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq


title: C2C12 myotubes treated with corticosterone 10-7M for 24H, rep3

value: cell line

value: WT

value: corticosterone 10-7M


title: Tumor2, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq


title: LargeIntestine, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

value: LargeIntestine


title: mouse neutrophil, 36h larvae imm, 01

description:
Library name: 25_36h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: BALB/cByJ

value: Imm

value: 36 hr


title: C2C12 myotubes treated with corticosterone 10-7M for 24H, rep2

value: myotubes


title: Wild-type Caki-1 cells, Replicate 1, H3K27ac (ChIP)

description: Library name: Caki-1 WT, Rep1, ChIP

value: Kidney

value: Renal cell carcinoma


title: C2C12 myotubes treated with corticosterone 10-7M for 24H, rep1


title: Gallbladder-BileDuct, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

value: Gallbladder-BileDuct


title: Cabozantinib-resistant Caki-1 cells, Replicate 1 (Input)

description: Library name: Caki-1 Resistant, Rep1, INPUT


title: Cabozantinib-resistant Caki-1 cells, Replicate 2 (Input)

description: Library name: Caki-1 Resistant, Rep2, INPUT


title: Heart, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

value: Heart

value: 8 months


title: Wild-type Caki-1 cells, Replicate 2 (Input)

description: Library name: Caki-1 WT, Rep2, INPUT


title: CAF,33aEV,H3K4me3,Input

city: wuhan

first: Wei

last: Yan

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

institute: Wuhan University

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
ChIP-seq reads were aligned to the mm10 genome assembly using  with bowtie2-align-s version 2.3.5.1
Data were filtered using cutadapt version 1.18 with parameters -u 10 -u -15 -U 10 -U -15 -m 30
peaks were called using macs2 2.1.1.20160309 with the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
Assembly: mm10
Supplementary files format and content: bigwig files were generated using deeptools 3.1.3; Scores represent RPKM

source_name: Breast cancer

growth_protocol: DMEM (Gibco) , 10% FBS ,  1% penicillin/streptomycin. CAFs were cultured at 37℃at 5% CO2.

extract_protocol:
CAF cells (5 × 106) plated into a 10 cm dish were cross-linked for 10 min at room temperature with 1% fina formaldehyde and then quenched with 0.125M of glycine for 5 min. Aspirated off the supernatant and adde PBS to wash the cells. The cross-linked cells were harvested with PBS and then centrifuged for 5 min at 500 ×g. Supernatant was discarded and the precipitates were lysed with lysis buffer (50 mM Tris-HCl, pH 8.0, 0.5 SDS, 5 mM EDTA). After centrifugation at 10,000 × g for 2 min at 4°C, the pellet was washed once with digestion buffer (50 mM Tris-HCl, pH 7.6, 1 mM CaCl2, 0.2% triton X-100), incubated in 500 μL digestion buffer with 3 μL MNase (NEB, M0247S) at 37°C for 20 min and quenched with 5 μL of 0.5 M EDTA. Samples were sonicate briefly and the supernatant was transferred to new tubes after centrifugation.
ChIP-seq libraries were constructed with ChIP and input DNA using VATHS Universal DNA Library Pre Kit for Illumina (Vazyme, ND606). Briefly, 50 μL of DNA (8-10 ng) was end-repaired for dA tailing, followed by adaptor ligation. Each adaptor was marked with a barcode of 8 bp DNA. Adaptor-ligated DNA was purified by AMPure XP beads (1:0.6) and then amplified by PCR of 9 cycles with the primer matching with adaptor universal part. Amplified DNA was purified again using AMPure XP beads (1:0.9) in 20 μL EB elution buffer. Fo multiplexing, libraries with different barcode were mixed with equal molar quantities (30-50 million reads per 560 library).

treatment_protocol: CAFs were treated with 231 EV，231-G EV and 231/miR33a EV.

value: Breast cancer

value: CAF

value: Bresat cancer CAF

tag: antibody


title: mouse neutrophil, 18h no-larvae imm, 06

description:
Library name: 22_18h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: Neutrophil

value: Male

value: 18 hr


title: Wild-type Caki-1 cells, Replicate 1 (Input)

description: Library name: Caki-1 WT, Rep1, INPUT


title: CAF,-GEV,H3K4me3,Input


title: CAF,231EV,H3K4me3,Input


title: mouse neutrophil, 18h no-larvae ctrl, 03

description:
Library name: 21_18h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: WT

value: BALB/cByJ

value: Ctrl


title: BoneMarrow, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: BoneMarrow

value: BoneMarrow


title: Neutrophil, I3_R

city: Suzhou

first: Yixuan

last: Zhang

address: No.9 Chongwen Road

institute: Suzhou University

description: Library name: Sample 6

data_processing:
Raw sequencing data were processed by Trim_galore (v0.6.4) to remove adapter sequences, low-quality reads, and short reads, yielding clean reads.
Bowtie2 (v2.4.2) was used to align reads to the corresponding rRNA database, and rRNA sequences were removed.
Read indexing and mapping to the human reference genome (GRCh38/hg38) were performed using Hisat2 (v2.0.0).
Followed by transcriptome assembly using StringTie (v2.1.4).
Gene expression levels were quantified using Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Assembly: GRCh38/hg38
Supplementary files format and content: The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2.

source_name: blood

growth_protocol: Cells were grown to maximum confluency prior to treatment.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme) and sequenced on the Illumina NovaSeq 6000 platform with a 150-bp paired-end sequencing strategy. Enrichment of mRNA, library construction, sequencing, and data analysis were performed on the Yunbios platform. Raw sequencing data were processed by Skewer (v0.2.2) and its quality was assessed with FastQC (v0.11.2). The sequencing reads had a length of 2×150 bp. Read indexing and mapping to the human reference genome (GRCh38/hg38) were performed using Hisat2 (v2.0.0), followed by transcriptome assembly using StringTie (v2.1.4). Gene expression levels were quantified using Fragments Per Kilobase of transcript per Million mapped reads (FPKM).

treatment_protocol: Neutrophils were collected from both the IFN-γ-stimulated group (experimental group) and the unstimulated group (control group).

value: blood

value: primary

value: Add IFN - γ to 1640 complete culture medium


title: Bladder, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: Bladder

value: Bladder


title: mouse neutrophil, 18h no-larvae imm, 05

description:
Library name: 20_18h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Imm


title: CAF,33aEV,H3K4me3,ChIP

value: Breast cancer


title: Thymus, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Thymus

value: Thymus

value: 8 months


title: mouse neutrophil, 18h no-larvae imm, 04

description:
Library name: 19_18h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous


title: CAF,-GEV,H3K4me3,ChIP

value: CAF

value: Bresat cancer CAF


title: Stomach, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

value: Stomach

value: Male


title: Neutrophil, I1_R

description: Library name: Sample 4

value: Neutrophil


title: CAF,231EV,H3K4me3,ChIP


title: mouse neutrophil, 18h no-larvae ctrl, 05

description:
Library name: 24_18h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Primary cells

value: WT

value: BALB/cByJ

value: 18 hr


title: Neutrophil, C3_R

description: Library name: Sample 3

value: blood

value: primary

value: 1640 complete culture medium


title: Spleen, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Spleen

value: Spleen


title: mouse neutrophil, 18h no-larvae ctrl, 04

description:
Library name: 23_18h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Ctrl


title: mouse neutrophil, 18h no-larvae imm, 03

description:
Library name: 17_18h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Imm


title: Brain, Trp53-/-_mouse_0514, 8_month-old

description: Microwell-based ATAC-seq

source_name: Brain

value: Brain

value: 8 months


title: Neutrophil, C2_R

description: Library name: Sample 2


title: mouse neutrophil, 18h no-larvae imm, 01

description:
Library name: 15_18h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous


title: mouse neutrophil, 18h no-larvae imm, 02

description:
Library name: 16_18h_NoLarvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description


title: Neutrophil, C1_R

description: Library name: Sample 1


title: Thymus,Trp53+/+_mouse_1101,17_week-old

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the BSTMatrixv software 1.9 (http://www.bmkmanu.com/wp-content/uploads/2022/10/BMKMANU-S1000-Library-Construction-Kit-User-Guide.pdf)
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: barcodes.tsv.gz: barcode name file, one barcode name per line, and each barcode represents a supSpot
Supplementary files format and content: barcodes_pos.tsv.gz: supSpot location file, tab split, the first column is the name of supSpot, and the second and third columns are the coordinates of supSpot on HE picture
Supplementary files format and content: barcodes_sequence.txt: barcode sequence file
Supplementary files format and content: features.tsv.gz: gene information file, tab division, the first column is gene ID, and the second column is gene name
Supplementary files format and content: matrix.mtx.gz:In the expression matrix file, the first column is the gene, the numerical value corresponds to the line number in features.tsv.gz file, the second column is supSpot, the numerical value corresponds to the line number in barcodes.tsv.gz file, and the third column is the umi number of the gene in this supSpot

extract_protocol:
The thymuses of Trp53-/- and Trp53+/+ mice were isolated and embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice.
Library preparations were performed with the BMKMANU S1000 protocol using Spatial transcriptomics Gene Expression Kit (BMKMANU, ST03002) and Tissue Optimization Kit (BMKMANU, ST03003)
stRNA-seq

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 ml cold PBS.

value: Thymus

value: 17 weeks

value: Female


title: Thymus,Trp53-/-_mouse_1308, 21_week-old

value: 21 weeks


title: SmallIntestine, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

value: SmallIntestine

value: Male


title: SalivaryGland, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

value: SalivaryGland


title: mouse neutrophil, 18h no-larvae ctrl, 02

description:
Library name: 14_18h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Primary cells

value: Neutrophil

value: WT

value: BALB/cByJ

value: 18 hr


title: Calu-3 treated with AdV1 (100 VP/mL), S-His, N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2. Rep 3

city: Warsaw

first: Monika

middle: Maria

last: Staniszewska

address: Poleczki 19

department: CEZAMAT

country: Poland

institute: Warsaw University of Technology

description:
Library name: Calu-3 AdV1+S+N rep3
“S15” column

data_processing:
Only reads that were longer than 35 nucleotides and properly paired were kept (cutadapt -m 35).
The reads were aligned to the human GRCh. 38 genome with GENCODE version 43 primary annotation, using the RSEM-1.3.3 pipeline coupled with STAR-2.7.10b (rsem-calculate-expression --star --star-path ~/STAR-2.7.10b --star-gzipped-read-file --paired-end --strandedness reverse -p 14 input.1.fastq.gz input.2.fastq.gz ./GRCH.38.gencode.v43.primary ./output/)
Assembly: human GRCh38
Supplementary files format and content: comma separated value text file with ENSEMBLE gene ID and RSEM estimated read count per gene for all samples

growth_protocol: 3D alveoli-like co-culture consisting of Calu-3 cells and PBMCs onto Corning® Transwell® Inserts. The Calu-3 cell line (1 × 10^5 cells/mL) was seeded onto Corning Transwell Inserts (700 µL of cell growth medium under the insert, 300 µL of cell suspension on the insert) and incubated for 72 h at 37°C with 5% CO2. Then, the culture medium was discarded to create an air-liquid interface, allowing the Calu-3 cells to form microvilli, as monitored by SEM. The cells were cultured for 14 days, with the medium exchange every 72 hours to stimulate the cell growth. After 14 days, PBMCs in a total volume of 700 µL (2.5–3 × 10^6 cells/mL in Opti-MEM) were added to the liquid site of the culture. The model prepared in this way was immediately used for further experiments.

extract_protocol:
RNA was extracted from cell pellets using the Total RNA Mini Kit (A&A Bio technology, Gdansk, Poland).
Strand-specific,  read length of 100bp in a paired-end mode, with rRNA depletion

treatment_protocol: PBMCs were seeded into 24-well plates in triplicate to study all immunogenic factors and incubated overnight at 37°C with 5% CO2. Then, the cell growth medium was replaced by 1 mL/well of the OptiMEM medium with reduced FBS concentration (5% v/v), and the immunogenic factors were added in the concentrations as follows: AdV1 (100 VP/cell, [10],  Spike-S1-His (0.25 µg/mL, InvivoGen USA), Nucleocapsid-His (0.25 µg/mL, InvivoGen USA),  AdV1+Spike-S1-His+Nucleocapsid-His (100 VP/cell+0.25 µg/mL+0.25 µg/mL). Plates were incubated for 7 days at 34.5°C with 5% CO2, and then the cells were collected for the immunophenotyping and apoptosis assay. The cell growth medium was collected and stored at -80 °C for cryopreservation before cytokine profiling.

value: Cellls treated with AdV1 (100 VP/mL), S-His, and N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2.