title: FIP-cat 18, study day 168

status: Public on Sep 17 2025

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description: Library name: 021_PAX-VB_D168_A1

data_processing:
Quality of the sequencing data was checked using FastQC (version 0.11.9)
RNA-seq reads were mapped against the domestic cat genome assembly (version Felis catus 9.0), rRNA sequences and the FCoV genome (NC_002306.3) using ContextMap 2 (version 2.7.9) (using BWA as short read aligner and with default parameters).
SAM output files of ContextMap2 were converted to BAM files using samtools.
Number of read fragments per gene were determined from BAM files in a strand-specific manner using featureCounts and gene annotations from Ensembl (version 106)
Assembly: Felis catus 9.0, NC_002306.3
Supplementary files format and content: tsv file containing normalized gene read counts (normalized with FPKM method)

organism: Felis catus

source_name: whole blood

extract_protocol:
RNA was extracted with the QIAsymphony PAXgene Blood RNA Kit. 200ng of total RNA was used as input for library preparation.
RNA-Seq libraries were generated using the NEBNext Ultra II Directional Library Prep Kit for Illumina, together with the NEBNext rRNA depletion Module, according to the manufacturer's protocol.

value: whole blood

tag: day of_treatment

tag: follow-up


title: FIP-cat 18, study day 28

type: SRA

city: München

country: Germany

description: Library name: 021_PAX-VB_D28_A1

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: Old.4h.A

status: Public on Sep 18 2025

city: Liverpool

first: Ufuk

last: Ersoy

address: William Henry Duncan Building

country: United Kingdom

institute: University of Liverpool

description:
Library name: Sample 1
Old replicate A
old_vs_young_RNA_kinetics.csv

data_processing:
The raw FASTQ files are trimmed to remove Illumina adapter sequences with Cutadapt version 4.5.
Reads shorter than 15 bp were discarded after trimming. Only read pairs were retained; if one read of a pair was removed, its mate was also discarded.
Reads were aligned to the Equus caballus EquCab3.0 primary assembly (Ensembl release 114) using STAR (version 2.5.3) with the following parameters: --outFilterMismatchNmax 40, --outFilterScoreMinOverLread 0.2, --outFilterMatchNminOverLread 0.2, --alignEndsType Extend5pOfReads12, and --outSAMattributes nM MD NH.
GEDI toolkit was utilised to merge and convert bam files into a CIT file (22) and then processed using GRAND-SLAM (version 2.0.7) to generate new-to-total RNA values (NTR) and read counts.
RNA synthesis rates and half-lives were estimated with the grandR using binomial distributions for reads from labelled and unlabelled RNAs.
Assembly: Equus caballus EquCab3.0 primary assembly (Ensembl release 114)
Supplementary files format and content: csv files containing RNA half-life and synthesis rate

organism: Equus caballus

source_name: Cartilage

growth_protocol: Chondrocytes were isolated from cartilage and cultured in complete DMEM for 2 days in a humidified atmosphere containing 5% CO₂ at 37°C.

extract_protocol:
RNA was extracted using TRIzol and chloroform, then alkylated with iodoacetamide (IAA) for 15 minutes at 50°C.
RNA libraries from submitted equine total RNA samples were performed using the NEBNext polyA selection and Ultra II Directional RNA library prep kits, (New England Biolabs, UK, #E7760S).

treatment_protocol: Cells were treated with 4sU for 4 hours

value: Cartilage

tag: cell type

value: chondrocyte

tag: age

value: old

tag: Sex

value: female

tag: genotype

value: WT

tag: treatment

value: 4-thiouridine (4sU) treated

tag: batch


title: FIP-cat 18, study day 2

description: Library name: 021_PAX-VB_D2_A1


title: FIP-cat 18, study day 7

description: Library name: 021_PAX-VB_D7_A1


title: FIP-cat 17, study day 7

description: Library name: 019_PAX-VB_D7_A1


title: FIP-cat 18, study day 0

description: Library name: 021_PAX-VB_D0_A1


title: FIP-cat 17, study day 28

description: Library name: 019_PAX-VB_D28_A1


title: FIP-cat 17, study day 2

description: Library name: 019_PAX-VB_D2_A1


title: FIP-cat 17, study day followup 2

description: Library name: 019_PAX-VB-FU2_A1


title: FIP-cat 18, study day followup 1

description: Library name: 021_PAX-VB-FU1_A1


title: FIP-cat 17, study day 0

description: Library name: 019_PAX-VB_D0_A1


title: FIP-cat 17, study day followup 1

description: Library name: 019_PAX-VB-FU1_A1


title: FIP-cat 18, study day followup 2

description: Library name: 021_PAX-VB-FU2_A1


title: FIP-cat 16, study day 168

description: Library name: 018_PAX-VB_D168_A1


title: B010 first branch, early flowering stage, rep2

city: Nanchang

first: Xinjie

last: Yuan

state: Jiangxi

address: No. 602, Nanlian Road

department: Institute of Vegetables and Flowers

country: China

institute: Jiangxi Academy of Agricultural Sciences

description: Library name: B010 rep 2

data_processing:
Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using using HISAT2. StringTie was used to count the reads numbers mapped to each gene.
Assembly: PRJNA788020
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

molecule: polyA RNA

organism: Capsicum annuum

source_name: first branch

extract_protocol:
RNA was harvested using RNAprep Pure Plant Plus Kit (TIANGEN), 1.0 μg of total RNA was used for the construction of secuencing libraries
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit (vazyme) following manufacturer's protocols

value: first branch


title: FIP-cat 16, study day 28

description: Library name: 018_PAX-VB_D28_A1


title: FIP-cat 16, study day 2

description: Library name: 018_PAX-VB_D2_A1


title: FIP-cat 16, study day followup 2

description: Library name: 018_PAX-VB-FU2_A1


title: FIP-cat 15, study day 168

description: Library name: 017_PAX-VB_D168_A1


title: FIP-cat 16, study day followup 1

description: Library name: 018_PAX-VB-FU1_A1


title: FIP-cat 16, study day 0

description: Library name: 018_PAX-VB_D0_A1


title: FIP-cat 15, study day 7

description: Library name: 017_PAX-VB_D7_A1


title: FIP-cat 16, study day 7

description: Library name: 018_PAX-VB_D7_A1


title: FIP-cat 15, study day 0

description: Library name: 017_PAX-VB_D0_A1


title: FIP-cat 15, study day followup 2

description: Library name: 017_PAX-VB-FU2_A1


title: FIP-cat 15, study day 28

description: Library name: 017_PAX-VB_D28_A1


title: FIP-cat 14, study day 28

description: Library name: 016_PAX-VB_D28_A1


title: FIP-cat 14, study day 7

description: Library name: 016_PAX-VB_D7_A1


title: FIP-cat 14, study day 168

description: Library name: 016_PAX-VB_D168_A1


title: FIP-cat 15, study day followup 1

description: Library name: 017_PAX-VB-FU1_A1


title: FIP-cat 17, study day 168

description: Library name: 019_PAX-VB_D168_A1


title: FIP-cat 14, study day 2

description: Library name: 016_PAX-VB_D2_A1


title: FIP-cat 14, study day 0

description: Library name: 016_PAX-VB_D0_A1


title: FIP-cat 13, study day 168

description: Library name: 015_PAX-VB_D168_A1


title: FIP-cat 13, study day 7

description: Library name: 015_PAX-VB_D7_A1


title: FIP-cat 13, study day 28

description: Library name: 015_PAX-VB_D28_A1


title: FIP-cat 13, study day 2

description: Library name: 015_PAX-VB_D2_A1


title: FIP-cat 13, study day 0

description: Library name: 015_PAX-VB_D0_A1


title: FIP-cat 13, study day followup 1

description: Library name: 015_PAX-VB-FU1_A1


title: FIP-cat 14, study day followup 1

description: Library name: 016_PAX-VB-FU1_A1


title: FIP-cat 14, study day followup 2

description: Library name: 016_PAX-VB-FU2_A1


title: FIP-cat 13, study day followup 2

description: Library name: 015_PAX-VB-FU2_A1


title: FIP-cat 12, study day 2

description: Library name: 014_PAX-VB_D2_A1


title: FIP-cat 12, study day 7

description: Library name: 014_PAX-VB_D7_A1


title: FIP-cat 12, study day 28

description: Library name: 014_PAX-VB_D28_A1


title: FIP-cat 12, study day 0

description: Library name: 014_PAX-VB_D0_A1


title: FIP-cat 12, study day followup 2

description: Library name: 014_PAX-VB-FU2_A1


title: FIP-cat 15, study day 2

description: Library name: 017_PAX-VB_D2_A1


title: FIP-cat 12, study day 168

description: Library name: 014_PAX-VB_D168_A1


title: FIP-cat 11, study day 2

description: Library name: 013_PAX-VB_D2_A1


title: FIP-cat 11, study day 168

description: Library name: 013_PAX-VB_D168_A1


title: FIP-cat 11, study day 0

description: Library name: 013_PAX-VB_D0_A1


title: FIP-cat 11, study day followup 2

description: Library name: 013_PAX-VB-FU2_A1


title: FIP-cat 11, study day 28

description: Library name: 013_PAX-VB_D28_A1


title: FIP-cat 11, study day followup 1

description: Library name: 013_PAX-VB-FU1_A1


title: FIP-cat 12, study day followup 1

description: Library name: 014_PAX-VB-FU1_A1


title: FIP-cat 11, study day 7

description: Library name: 013_PAX-VB_D7_A1


title: FIP-cat 10, study day 168

description: Library name: 012_PAX-VB_D168_A1


title: FIP-cat 10, study day 7

description: Library name: 012_PAX-VB_D7_A1


title: FIP-cat 10, study day 2

description: Library name: 012_PAX-VB_D2_A1


title: FIP-cat 10, study day 0

description: Library name: 012_PAX-VB_D0_A1


title: FIP-cat 10 study day followup 1

description: Library name: 012_PAX-VB-FU1_A1


title: FIP-cat 9, study day 168

description: Library name: 010_PAX-VB_D168_A1


title: FIP-cat 9, study day 7

description: Library name: 010_PAX-VB_D7_A1


title: FIP-cat 9, study day 28

description: Library name: 010_PAX-VB_D28_A1


title: DLK2-OE1, replicate 3

city: Beijing

first: Nie Xiaofan

last: NieXiaofan

address: 北京市怀柔区怀北镇怀北庄380号

institute: University of Chinese Academy of Sciences

description: Library name: DLK2-OE1-3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments. Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Assembly: tair_TAIR10
Supplementary files format and content: The txt files include the AGI code, count and FPKM for each sample.

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: 11-day-old WT and DLK2-OE1 seedlings were transferred from 1/2 Murashige and Skoog (MS) plates to soil and grown for 13 additional day.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired. A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X).And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000.

treatment_protocol: The rosette leaves of 24-day-old WT and DLK2-OE1 seedlings were frozen in liquid nitrogen immediately.

value: Rosette leaves


title: DLK2-OE1, replicate 4

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: DLK2-OE1-4


title: FIP-cat 9, study day 2

description: Library name: 010_PAX-VB_D2_A1


title: DLK2-OE1, replicate 2

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: DLK2-OE1-2


title: DLK2-OE1, replicate 1

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: DLK2-OE1-1


title: FIP-cat 9, study day 0

description: Library name: 010_PAX-VB_D0_A1


title: WT, replicate 2

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: WT-2


title: FIP-cat 8, study day 168

description: Library name: 009_PAX-VB_D168_A1


title: WT, replicate 1

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: WT-1


title: FIP-cat 8, study day 7

description: Library name: 009_PAX-VB_D7_A1


title: plt3plt5plt7pin1T600I BC1F2 pheno+ pool

city: Wageningen

first: Merijn

last: Kerstens

address: Droevendaalsesteeg 1

department: Plant Developmental Biology

country: Netherlands

institute: Wageningen University & Research

description: Library name: plt3plt5plt7pin1T600I pheno+

library_source: genomic

data_processing:
Adapter trimming was performed with fastp v0.23.2, specifying --trim_poly_g.
Reads were mapped to the reference genome with BWA-MEM v0.7.17.
Readgroups were assigned with picard v2.27.2 AddOrReplaceReadGroups, and duplicates were removed with picard MarkDuplicates.
Variants were called with GATK v4's HaplotypeCaller.
Assembly: TAIR10
Supplementary files format and content: VCF files with raw called variants per pool

molecule: genomic DNA

source_name: leaf

growth_protocol: plt3plt5plt7 and BC1F2 plt3plt5plt7EMS (identified allele: pin1T600I) seedlings were grown for 6-8 weeks on soil in a long day (16 h light, 8 h dark) growth chamber at 22 degrees, until the inflorescence phenotypes appeared.

extract_protocol:
Per pool, young leaf material of 30 plants was collected on ice, then ground with a metal ball in a TissueLyzer LT (Qiagen). CTAB DNA extraction was used on the remaining powder.
NEBNext® Ultra II DNA Library Prep kit for Illumina.

value: leaf

value: plt3plt5plt7pin1T600I pheno+

tag: generation

tag: phenotype

value: mutant


title: FIP-cat 8, study day 2

description: Library name: 009_PAX-VB_D2_A1


title: FIP-cat 10, study day 28

description: Library name: 012_PAX-VB_D28_A1


title: plt3plt5plt7 backcross parent

description: Library name: plt3plt5plt7

value: backcross parent


title: 3xFLAG-GFP_DAP_IM_rep2

description: Library name: GFP_DAP_IM_2

data_processing:
Adapter trimming was performed with fastp v0.23.2, specifying --trim_poly_g.
Reads were mapped to the reference genome with BWA-MEM v0.7.17.
Unmapped, duplicate, and mapping quality < 30 reads were removed with SAMtools v1.15 and Sambamba v0.6.6.
Peaks were called separately for each sample (incl. GFP) with MACS3 v3 at a q-value = 0.1 cutoff.
Assembly: TAIR10
Supplementary files format and content: Narrowpeaks files per sample with peak locations

source_name: inflorescence meristem

growth_protocol: Col-0 seedlings were grown for 9 days (SAMs) on 1/2MS medium + 1% agar on top of a nylon mesh, or 4-8 weeks on soil (IM) in a long day (16 h light, 8 h dark) growth chamber at 22 degrees.

extract_protocol:
Per replicate, 500 SAMs or IMs were collected on ice, then ground with a metal ball in a TissueLyzer LT (Qiagen). CTAB DNA extraction was used on the remaining powder.
DAP-seq libraries were prepared according to Bartlett et al., (2017) with Illumina TruSeq barcodes. 100 ng of gDNA was used as starting material. Libraries were amplified using 15 cycles. Post-amplification libraries were size selected at >200 bp in length using AMPure XP beads.

value: inflorescence meristem

tag: dap protein

tag: replicate


title: FIP-cat 8 study day followup 1

description: Library name: 009_PAX-VB-FU1_A1


title: plt3plt5plt7pin1T600I BC1F2 pheno- pool

description: Library name: plt3plt5plt7pin1T600I pheno-

value: plt3plt5plt7pin1T600I pheno-

value: wild type


title: FIP-cat 7, study day 28

description: Library name: 008_PAX-VB_D28_A1


title: 3xFLAG-GFP_DAP_IM_rep1

description: Library name: GFP_DAP_IM_1


title: FIP-cat 7, study day 168

description: Library name: 008_PAX-VB_D168_A1


title: 3xFLAG-PLT7_DAP_IM_rep2

description: Library name: PLT7_DAP_IM_2


title: WT, replicate 4

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: WT-4


title: 3xFLAG-PLT7_DAP_IM_rep1

description: Library name: PLT7_DAP_IM_1


title: 3xFLAG-PLT5_DAP_IM_rep2

description: Library name: PLT5_DAP_IM_2


title: WT, replicate 3

address: 北京市怀柔区怀北镇怀北庄380号

description: Library name: WT-3


title: FIP-cat 7, study day 0

description: Library name: 008_PAX-VB_D0_A1


title: FIP-cat 7, study day followup 2

description: Library name: 008_PAX-VB-FU2_A1


title: 3xFLAG-PLT3_DAP_IM_rep1

description: Library name: PLT3_DAP_IM_1


title: FIP-cat 7, study day 7

description: Library name: 008_PAX-VB_D7_A1


title: 3xFLAG-PLT3_DAP_IM_rep2

description: Library name: PLT3_DAP_IM_2


title: FIP-cat 8, study day 28

description: Library name: 009_PAX-VB_D28_A1


title: FIP-cat 7 study day followup 1

description: Library name: 008_PAX-VB-FU1_A1


title: FIP-cat 6, study day 168

description: Library name: 006_PAX-VB_D168_A1


title: FIP-cat 6, study day 28

description: Library name: 006_PAX-VB_D28_A1


title: 3xFLAG-GFP_DAP_SAM_rep1

description: Library name: GFP_DAP_SAM_1

source_name: shoot apical meristem

value: shoot apical meristem


title: FIP-cat 8, study day 0

description: Library name: 009_PAX-VB_D0_A1

value: whole blood


title: FIP-cat 6, study day 7

description: Library name: 006_PAX-VB_D7_A1


title: FIP-cat 8, study day followup 2

description: Library name: 009_PAX-VB-FU2_A1


title: 3xFLAG-PLT7_DAP_SAM_rep1

description: Library name: PLT7_DAP_SAM_1


title: FIP-cat 6, study day 2

description: Library name: 006_PAX-VB_D2_A1


title: 3xFLAG-PLT7_DAP_SAM_rep2

description: Library name: PLT7_DAP_SAM_2


title: FIP-cat 6, study day followup 2

description: Library name: 006_PAX-VB-FU2_A1


title: FIP-cat 6, study day 0

description: Library name: 006_PAX-VB_D0_A1


title: FIP-cat 6 study day followup 1

description: Library name: 006_PAX-VB-FU1_A1


title: 3xFLAG-PLT5_DAP_SAM_rep1

description: Library name: PLT5_DAP_SAM_1


title: 3xFLAG-PLT3_DAP_SAM_rep2

description: Library name: PLT3_DAP_SAM_2


title: 3xFLAG-PLT5_DAP_SAM_rep2

description: Library name: PLT5_DAP_SAM_2


title: 3xFLAG-PLT5_DAP_IM_rep1

description: Library name: PLT5_DAP_IM_1


title: FIP-cat 5, study day 168

description: Library name: 005_PAX-VB_D168_A1


title: FIP-cat 5, study day 28

description: Library name: 005_PAX-VB_D28_A1


title: FIP-cat 5, study day 7

description: Library name: 005_PAX-VB_D7_A1


title: trb1-2-3_H3K4me3_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

description: Library name: Sample 37

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, under a 8 h light/16 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: Arabidopsis seedlings

tag: chip antibody

value: Abcam, ab8580


title: trb1-2-3_H3K4me3_rep1

description: Library name: Sample 36


title: 3xFLAG-GFP_DAP_SAM_rep2

description: Library name: GFP_DAP_SAM_2


title: jmj14_H3K4me3_rep1

description: Library name: Sample 34


title: FIP-cat 5, study day followup 1

description: Library name: 005_PAX-VB-FU1_A1


title: FIP-cat 4, study day 28

description: Library name: 004_PAX-VB_D28_A1


title: 3xFLAG-PLT3_DAP_SAM_rep1

description: Library name: PLT3_DAP_SAM_1


title: icu11_H3K4me3_rep1

description: Library name: Sample 32


title: FIP-cat 5, study day followup 2

description: Library name: 005_PAX-VB-FU2_A1


title: icu11_H3K4me3_rep2

description: Library name: Sample 33


title: FIP-cat 4, study day 0

description: Library name: 004_PAX-VB_D0_A1


title: hth1_H3K4me3_rep1

description: Library name: Sample 30

value: hth1-/- (in Col-0)


title: FIP-cat 4, study day 2

description: Library name: 004_PAX-VB_D2_A1


title: jmj14_H3K4me3_rep2

description: Library name: Sample 35


title: Wildtype_Col-0_H3K4me3_rep2

description: Library name: Sample 29

value: wild type (in Col-0)


title: Wildtype_Col-0_H3K4me3_rep1

description: Library name: Sample 28


title: FIP-cat 4, study day 168

description: Library name: 004_PAX-VB_D168_A1


title: FIP-cat 4, study day 7

description: Library name: 004_PAX-VB_D7_A1


title: FIP-cat 4, study day followup 2

description: Library name: 004_PAX-VB-FU2_A1


title: FIP-cat 4, study day followup 1

description: Library name: 004_PAX-VB-FU1_A1


title: FIP-cat 3, study day 28

description: Library name: 003_PAX-VB_D28_A1


title: FIP-cat 3, study day 168

description: Library name: 003_PAX-VB_D168_A1


title: IP_TRB1-del-Myb_FLAG_rep2

description: Library name: Sample 27

value: SIGMA, F1804

value: 1305-TRB1-delMyb-FLAG transformed plants (in Col-0)


title: FIP-cat 3, study day 0

description: Library name: 003_PAX-VB_D0_A1


title: FIP-cat 3, study day 7

description: Library name: 003_PAX-VB_D7_A1


title: Input_TRB1-del-Myb_FLAG

description: Library name: Sample 25


title: IP_TRB1-del-Myb_FLAG_rep1

description: Library name: Sample 26


title: FIP-cat 2, study day 168

description: Library name: 002_PAX-VB_D168_A1


title: IP_TRB1-del-GH1_FLAG_rep2

description: Library name: Sample 24

value: 1305-TRB1-delGH1-FLAG transformed plants (in Col-0)


title: Input_TRB1-del-GH1_FLAG

description: Library name: Sample 22


title: FIP-cat 2, study day 28

description: Library name: 002_PAX-VB_D28_A1


title: IP_TRB1-WT_FLAG_rep2

description: Library name: Sample 21

value: 1305-TRB1-WT-FLAG transformed plants (in Col-0)


title: FIP-cat 2, study day 0

description: Library name: 002_PAX-VB_D0_A1


title: IP_TRB1-WT_FLAG_rep1

description: Library name: Sample 20


title: FIP-cat 2, study day followup 2

description: Library name: 002_PAX-VB-FU2_A1


title: IP_ZDP2_FLAG_rep2

description: Library name: Sample 18

value: 1305-ZDP2-FLAG transformed plants (in Col-0)


title: Input_TRB1-WT_FLAG

description: Library name: Sample 19


title: FIP-cat 2, study day followup 1

description: Library name: 002_PAX-VB-FU1_A1


title: Input_ZDP2_FLAG

description: Library name: Sample 16


title: FIP-cat 1, study day 28

description: Library name: 001_PAX-VB_D28_A1


title: IP_TRB1_FLAG_rep1

description: Library name: Sample 14

value: 1305-TRB1-FLAG transformed plants (in Col-0)


title: IP_ZDP2_FLAG_rep1

description: Library name: Sample 17


title: FIP-cat 1, study day 168

description: Library name: 001_PAX-VB_D168_A1


title: FIP-cat 1, study day 7

description: Library name: 001_PAX-VB_D7_A1


title: Input_TRB1_FLAG

description: Library name: Sample 13


title: FIP-cat 1, study day 0

description: Library name: 001_PAX-VB-D0_A1


title: IP_NAC52_FLAG_rep2

description: Library name: Sample 12

value: 1305-NAC52-FLAG transformed plants (in Col-0)


title: IP_TRB1-del-GH1_FLAG_rep1

description: Library name: Sample 23


title: IP_NAC52_FLAG_rep1

description: Library name: Sample 11


title: FCoV-positive healthy control cat 11

description: Library name: 011_Kp_PAX-A1


title: FCoV-positive healthy control cat 10

description: Library name: 010_Kp_PAX-A1


title: Input_NAC52_FLAG

description: Library name: Sample 10


title: FIP-cat 2, study day 7

description: Library name: 002_PAX-VB_D7_A1


title: IP_JMJ14_FLAG_rep2

description: Library name: Sample 9

value: 1305-JMJ14-FLAG transformed plants (in Col-0)


title: IP_JMJ14_FLAG_rep1

description: Library name: Sample 8


title: FCoV-positive healthy control cat 8

description: Library name: 008_Kp_PAX-A1


title: FIP-cat 2, study day 2

description: Library name: 002_PAX-VB_D2_A1


title: FCoV-positive healthy control cat 7

description: Library name: 007_Kp_PAX-A1


title: Input_JMJ14_FLAG

description: Library name: Sample 7


title: KO Lung, 500ng IL-33, 4 days, RNA-seq, replicate2

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: ILC2eff KO2

data_processing:
RNA-seq data were analyzed using the Galaxy web platform public server (https://usegalaxy.org). Briefly, quality-filtered reads performed using “fastp” were mapped to the mouse genome (mm10) by “HISAT2” (Galaxy Version 2.2.1). Gene raw counts were analyzed by “FeatureCounts” (Galaxy Version 2.0.1) and genes were annotated by “annotateMyIDs” (Galaxy Version 3.12.0). Differential gene expression was analyzed by EdgeR (Galaxy Version 3.34.0) and differentially expressed genes were picked based on three criteria: 1) The genes were protein-coding genes; 2) significance level p < 0.05; 3) differential mRNA expression for more than 1.2 fold.
Assembly: mm10
Supplementary files format and content: Excel, geneID, raw counts

organism: Mus musculus

source_name: lung

extract_protocol:
Lung ILC2s (Lin−CD45+RFP+ cells) were purified from IL-33 treated Il5Cre/+Smarca4+/+(WT) and Il5Cre/+Smarca4f/f (KO) mice. Each biological repeat was 2×105cells pooled from 3-12 mice. The sample RNA was extracted with TRIzol reagent.
Construction of the cDNA library and transcriptome sequencing were performed by BGI Genomics, BGI-Shenzhen. Generally, total RNA was treated with DNase I and purified with magnetic beads with Oligo (dT) to isolate mRNA. Treated with the fragmentation buffer, mRNA was fragmented into short fragments, which were the templates of cDNA library. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. Then, the short fragments are connected with adapters and suitable fragments were selected for the PCR amplification. Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were used for quantification and qualification of the cDNA library.

value: lung

tag: cell line

value: Lin-CD45+RFP+ cells

value: 500ng IL-33, i.p, 4 days


title: KO Lung, 500ng IL-33, 4 days, RNA-seq, replicate1

description: ILC2eff KO1


title: IP_TRB1_FLAG_rep2

description: Library name: Sample 15


title: FCoV-positive healthy control cat 6

description: Library name: 006_Kp_PAX-A1


title: IP_ICU11_FLAG_rep1

description: Library name: Sample 5

value: 1305-ICU11-FLAG transformed plants (in Col-0)


title: WT Lung, 500ng IL-33, 4 days, RNA-seq, replicate2

description: ILC2eff WT2


title: Input_ICU11_FLAG

description: Library name: Sample 4


title: FCoV-positive healthy control cat 5

description: Library name: 005_Kp_PAX-A1

value: whole blood


title: WT Lung, 500ng IL-33, 4 days, RNA-seq, replicate1

description: ILC2eff WT1


title: Lung, 30ng papain, 3 days, RNA-seq, replicate2

extract_protocol:
Female mice were used for library construction. Lung ILC2s (Lin−CD25+ST2+ cells) were sorted by flow cytometry (Beckman Coulter) respectively from naïve (as ILC2nav) or papain-treated (50 μg/day for 3 days) mice (as ILC2eff).
Construction of the cDNA library and transcriptome sequencing were performed by BGI Genomics, BGI-Shenzhen. Generally, total RNA was treated with DNase I and purified with magnetic beads with Oligo (dT) to isolate mRNA. Treated with the fragmentation buffer, mRNA was fragmented into short fragments, which were the templates of cDNA library. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. Then, the short fragments are connected with adapters and suitable fragments were selected for the PCR amplification. Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were used for quantification and qualification of the cDNA library.

value: Lin-CD25+ST2+ cells

value: wild-type

value: 30ug papain, i.n, 3 days


title: FCoV-positive healthy control cat 12

description: Library name: 012_Kp_PAX-A1


title: FCoV-positive healthy control cat 4

description: Library name: 004_Kp_PAX-A1


title: Lung, 30ng papain, 3 days, RNA-seq, replicate1


title: IP_HTH1_FLAG_rep2

description: Library name: Sample 3

value: Arabidopsis seedlings

value: 1305-HTH1-FLAG transformed plants (in Col-0)


title: FCoV-positive healthy control cat 3

description: Library name: 003_Kp_PAX-A1


title: Lung, PBS, 3 days, RNA-seq, replicate2

value: PBS, i.n, 3 days


title: FCoV-positive healthy control cat 9

description: Library name: 009_Kp_PAX-A1


title: FCoV-positive healthy control cat 2

description: Library name: 002_Kp_PAX-A1


title: Lung, PBS, 3 days, RNA-seq, replicate1


title: IP_HTH1_FLAG_rep1

description: Library name: Sample 2

value: SIGMA, F1804


title: Input_HTH1_FLAG

description: Library name: Sample 1


title: FCoV-positive healthy control cat 1

description: Library name: 001_Kp_PAX-A1


title: over expression TRIM49 of NuGc3 replication 2

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

institute: Army Medical University (Third Military Medical University)

description: Library name: RNA-seq_NuGC3-oE49-rep2

data_processing:
RNA-seq were filtered by fastp (version 0.20.1). The cleaned reads of RNA-seq were aligned against the hg38 transcriptome using HISAT214 (version 2.1.0) and quantitated with featureCounts. The gene expression were normalized to TPM with our in-house scripts. Low expression genes were filtered and raw count matrix was used for differential expression analysis using edgeR (version 3.28.1). Differential expressed genes (DEGs) were set as FDR < 0.05 and |log2 FoldChange| > 0.58. The clusterProfiler package in R (version 3.6.1) was implemented to perform GO and KEGG pathway enrichment analyses of those DEGs.
The adaptor and low quality bases were removed by using fastp. The clean reads were mapped to human genome hg38 by using bowtie2 with the following parameter ”--end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 2000”. The duplicated reads were removed by using picard. The correlation of replicates were computed and visualized by using deeptools. Then we merged the two replicates of Galectin-3 and EGR1 respectively. Further, peaks were detected by using callpeak method of MACS2 with parameters “-f BAMPE -g hs --nolambda --nomodel --extsize 180 -q 0.05”. The peaks were annotation by using ChIPseeker. The ngs.plot.r was implemented to visualize the distribution of binding signal of Galectin-3 and EGR1. Additionally, Integrative Genomics Viewer (IGV) was implemented to visualize the binding signal of the specific location.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for RNA-seq
Supplementary files format and content: tab-delimited text files include peaks for Cut&Tag

organism: Homo sapiens

extract_protocol:
The poly (A)(+) messenger RNA (mRNA)  was enriched by Oligo dT
And then quantiﬁed and quality controlled by Agilent Bioanalyzer 2100 system. After cDNA library construction, the library preparations were sequenced on BGISEQ500 platform (BGI). The Cut&Tag expreiments were processed with Hyperactive Universal CUT&Tag Assay Kit from Vazyme and sequenced on Illumina platform.

value: Human gastric cancer

value: OE

value: Over expression TRIM49


title: over expression TRIM49 of NuGc3 replication 1

description: Library name: RNA-seq_NuGC3-oE49-rep1


title: IP_ICU11_FLAG_rep2

description: Library name: Sample 6


title: WT of NuGc3 replication 3

description: Library name: RNA-seq_NuGC3-WT-rep3

value: WT

value: DMSO


title: trb1-2-3_RNAseq_rep3

description: Library name: Sample 18

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000 platform, paired-end 150bp).

tag: time


title: FCoV-negative healthy control cat 5

description: Library name: 007_Kn_PAX-A1


title: WT of NuGc3 replication 1

description: Library name: RNA-seq_NuGC3-WT-rep1


title: trb1-2-3_RNAseq_rep2

description: Library name: Sample 17


title: Gac3 ihibition of NuGc3 replication 3

description: Library name: RNA-seq_NuGc3-shGac3-rep3

value: sh


title: FCoV-negative healthy control cat 4

description: Library name: 006_Kn_PAX-A1


title: trb1-2-3_RNAseq_rep1

description: Library name: Sample 16


title: FCoV-negative healthy control cat 3

description: Library name: 003_Kn_PAX-A1


title: Gac3 ihibition of NuGc3 replication 1

description: Library name: RNA-seq_NuGc3-shGac3-rep1


title: Wild type of NuGc3 replication 3

description: Library name: RNA-seq_NuGc3-ctrl-rep3


title: nac50-52_RNAseq_rep3

description: Library name: Sample 15


title: Wild type of NuGc3 replication 2

description: Library name: RNA-seq_NuGc3-ctrl-rep2


title: FCoV-negative healthy control cat 2

description: Library name: 002_Kn_PAX-A1


title: Wild type of NuGc3 replication 1

description: Library name: RNA-seq_NuGc3-ctrl-rep1


title: nac50-52_RNAseq_rep2

description: Library name: Sample 14


title: over expression TRIM49 of NuGc3 replication 3

description: Library name: RNA-seq_NuGC3-oE49-rep3


title: FCoV-negative healthy control cat 1

description: Library name: 001_Kn_PAX-A1


title: nac50-52_RNAseq_rep1

description: Library name: Sample 13


title: jmj14_RNAseq_rep3

description: Library name: Sample 12


title: R55 M-MDSC co-incubated Vdelta2 T cells

city: Lublin

first: Michal

last: Zarobkiewicz

address: Chodzki 4a

department: Clinical Immunology

country: Poland

institute: Medical University of Lublin

description: Library name: R55_MDSC_exposed

data_processing:
Raw read quality was assessed with FastQC; all samples passed. Reads were aligned to the human genome GRCh38 using STAR (RNAStar) with default RNA-seq settings, using GENCODE v44 reference. Gene-level counts were generated with featureCounts. Differential expression was performed in DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Vdelta2 T cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) from healthy adult donors were isolated by density‐gradient centrifugation. Vδ2 γδ T cells were expanded with zoledronate and IL-2 in RPMI-1640 supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 10 mM HEPES, and penicillin/streptomycin, at 37 °C, 5% CO₂. Cells were maintained at 0.5–1.0×10⁶ cells/mL with fresh medium/cytokine replenishment as needed for expansion.

extract_protocol:
Cells were collected and washed twice with PBS. Total RNA was isolated using the Total RNA Isolation Kit (Blirt, Gdańsk, Poland) according to the manufacturer’s instructions. Purified RNA was frozen at –80 °C until shipment for sequencing.
Qualified RNA was processed for library construction. mRNA was isolated using Oligo(dT)-attached magnetic beads and randomly fragmented. First-strand cDNA was synthesized using random hexamers, followed by second-strand synthesis with PCR buffer, dNTPs, RNase H, and DNA polymerase I. Double-stranded cDNA was purified with AMPure XP beads, end-repaired, A-tailed, and ligated to sequencing adapters. Fragments of 300–400 bp were size-selected with AMPure XP beads. Libraries were amplified by PCR and purified. Quality control was performed using Qubit 2.0 and Agilent 2100 for concentration and insert size assessment, and qPCR for accurate quantification. Libraries with concentration >2 nM were deemed acceptable for sequencing.

treatment_protocol: For co-culture conditions, autologous M-MDSC (CD14⁺/CD11b⁺/CD15⁻/HLA-DR^low) were generated from monocytes from the same donors and added to Vδ2 γδ T cells at a 2:1 (γδ T : M-MDSC) ratio in the same culture medium using plates with inserts. For vitamin treatment, phospho-vitamin C was added to zoledronate-expanded Vδ2 γδ T-cell cultures. Control cultures consisted of zoledronate-expanded Vδ2 γδ T cells without M-MDSC or vitamin C.

value: Vdelta2 T cells

value: M-MDSC exposed


title: R54 vitamin C treated Vdelta2 T cells

description: Library name: R54_vitc_treated

value: vitamin C


title: R57 M-MDSC co-incubated Vdelta2 T cells

description: Library name: R57_MDSC_exposed


title: R54 M-MDSC co-incubated Vdelta2 T cells

description: Library name: R54_MDSC_exposed


title: R53 vitamin C treated Vdelta2 T cells

description: Library name: R53_vitc_treated


title: WT of NuGc3 replication 2

description: Library name: RNA-seq_NuGC3-WT-rep2


title: PH 015

city: Hannover

first: Andrea

last: Hoffmann

address: Stadtfelddamm, 34

department: Orthopedic Surgery

institute: MHH

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.4.2) which is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The genome reference and annotation data were taken from GENCODE.org (Homo sapiens: GRCh38.p13; release 34).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”). Analysis was performed with multiple levels of primary factor (all different conditions) comparing all levels against each other.
Assembly: GRCh38.p13; release 34
Supplementary files format and content: txt file with DESeq2 normalized gene counts

source_name: bone marrow

growth_protocol: The bone marrow derived mesenchymal stem cells were cultured in MSC-GM growth medium (DMEM with 1 g/L D-glucose, with 3.7 g/L NaHCO3, with L-alanyl-L-gutamine (Sigma #FG0415) supplemented with 10 % FCS, 25 mM HEPES, 100000 U/L Penicillin, 100 mg/L Streptomycin, 2 mg/L FGF-2). The cells were incubated at 37 °C and 5 % CO2. The growth medium was changed twice a week. For sub cultivation of the cells trypsin was used to detach the cells. 2000 BM-MSCs per cm2 were seeded into a new cell culture flask.

extract_protocol:
Bone marrow (BM) was collected from the proximal femur during THA or from the distal femur during TKA. During these procedures, bone marrow was extruded and collected into syringes containing heparin (2,500 IU/mL heparin per 10 mL of bone marrow). The bone marrow preparations were further diluted fourfold with phosphate-buffered saline without Ca2+, Mg2+ (PBS). Samples were filtered through a 100-µm cell strainer to remove bone debris and then slowly applied to the density gradient material using a ratio of 1 volume of Biocoll (Biochrom, Berlin, Germany, L6115; ρ = 1.077 g/ml) to 2 Volumes of diluted bone marrow in 50 ml conical centrifuge tubes were used. After centrifugation at 500 × g for 30 min at room temperature without braking, mononuclear cells were collected from the density gradient. The mononuclear cells were washed once with PBS, followed by centrifugation at 500 × g for 5 min at room temperature with brakes. The cell pellet was resuspended in MSC-GM growth medium (DMEM with 1 g/L D-glucose, with 3.7 g/L NaHCO3, with L-alanyl-L-gutamine (Sigma #FG0415) supplemented with 10% FCS, 25 mM, resuspended HEPES, 100,000 U/L penicillin, 100 mg/L streptomycin, 2 mg/L FGF-2). Cells were seeded into tissue culture plastic bottles at a density of 500,000 mononuclear cells per cm2. The cells were incubated at 37 °C and 5% CO2. The next day, the medium was changed to remove nonadherent cells. For RNA-Seq, MSCs were cultured until reaching passage 3 (medium changed twice per week; trypsin was used for subculture). RNA was extracted from the BM-MCS using Trizol reagent (Invitrogen: 1 ml per 25 cm2 culture surface). The lysate was stored at −80°C until analysis. After thawing, 1/10 volume of 1-bromo-3-chloropropane was added and mixed by inverting. After incubation for 5 minutes at room temperature, the suspension was centrifuged for 15 minutes at 20,000 × g at 4 °C. The clear, colorless upper phase containing the RNA was transferred to a new tube and mixed gently with 0.6 volume of isopropanol. After a short incubation of 5 minutes, the suspension was centrifuged for 30 minutes at 20,000 × g at 4 °C. The resulting pellet was washed twice with ice-cold 80% ethanol (20,000 × g; 4 °C; 15 min). After drying, the pellet was resuspended in RNase-free water and incubated at 58 °C for 10 minutes.
Library generation, quality control, and quantification:  300ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes. cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 8 of final pcr. One additional purification step was introduced at the end of the standard procedure, using 1.2x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific). Library denaturation and Sequencing run: Equal molar amounts of individually barcoded libraries were pooled for, in total, 2 sequencing runs in which each analyzed library constituted around 7.8% of overall flowcell / run capacity. The library pool was denatured with NaOH and was finally diluted to 1.8pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3ml of the denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell (400M cluster) for single reads (20024906; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 38 bases each; Index reads 1 and 2 with 8 bases each.

value: bone marrow

tag: condition

value: primary

value: male

value: mesenchymal stem cells

tag: disease state

value: coxarthritis


title: jmj14_RNAseq_rep2

description: Library name: Sample 11

value: Arabidopsis seedlings


title: R55 untreated control Vdelta2 T cells

description: Library name: R55_control

value: control


title: Gac3 ihibition of NuGc3 replication 2

description: Library name: RNA-seq_NuGc3-shGac3-rep2


title: jmj14_RNAseq_rep1

description: Library name: Sample 10


title: R54 untreated control Vdelta2 T cells

description: Library name: R54_control


title: R53 M-MDSC co-incubated Vdelta2 T cells

description: Library name: R53_MDSC_exposed


title: R53 untreated control Vdelta2 T cells

description: Library name: R53_control


title: R58 M-MDSC co-incubated Vdelta2 T cells

description: Library name: R58_MDSC_exposed


title: icu11_RNAseq_rep3

description: Library name: Sample 9


title: PK 020

value: gonarthritis


title: PK 012

value: female


title: R58 untreated control Vdelta2 T cells

description: Library name: R58_control


title: icu11_RNAseq_rep2

description: Library name: Sample 8


title: R57 untreated control Vdelta2 T cells

description: Library name: R57_control


title: RK 017

value: revision

value: aseptic knee implant loosening


title: MHCC97H cells,pGreen-628,rep3

city: Chongqing

first: Lele

last: Liu

address: Yuzhong District Shiyou Road Street

institute: Chongqing Medical University

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to Human genome (GRCh38, Ensembl104) using the Hisat2. [Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 2015. April;12(4):357–360. doi: 10.1038/nmeth.3317] HTseq [Anders S, Pyl P T, Huber W. HTSeq–A Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2014: btu638.] was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: hg38
Supplementary files format and content: an LIST format file of gene expression profile based on FPKM method

source_name: Liver

growth_protocol: MHCC97H and Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Trizol was mixed with chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

value: Liver

value: hepatocellular carcinoma cells

value: miR-628-3p overexpression


title: MHCC97H cells,pGreen-628,rep2


title: PH 018


title: icu11_RNAseq_rep1

description: Library name: Sample 7


title: MHCC97H cells,pGreen-628,rep1


title: MHCC97H cells,vector,rep3

value: WT


title: RK 014


title: hth1_RNAseq_rep3

description: Library name: Sample 6


title: MHCC97H cells,vector,rep1


title: MHCC97H cells,vector,rep2


title: RK 015


title: Huh7 cells,mimics,rep3


title: hth1_RNAseq_rep2

description: Library name: Sample 5


title: Huh7 cells,mimics,rep2


title: hth1_RNAseq_rep1

description: Library name: Sample 4


title: Huh7 cells,mimics,rep1


title: PH 011


title: RK 008


title: Wildtype_Col-0_RNAseq_rep2

description: Library name: Sample 2

value: wild type Col-0


title: Huh7 cells,mimics-NC,rep3


title: Huh7 cells,mimics-NC,rep2


title: Wildtype_Col-0_RNAseq_rep3

description: Library name: Sample 3


title: Wildtype_Col-0_RNAseq_rep1

description: Library name: Sample 1


title: KO 1

first: Youqin

last: Zhang

address: No. 280, Chongqing South Road

institute: NewsMORE+  Shanghai Institute of Immunology

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: fpkm

extract_protocol:
ILC2s from epididymal adipose tissue were sorted.Total RNA was extracted from 2000-4000 cells using RNeasy Micro kit (QIAGEN, GER) according to the manual instruction.High quality RNA was used for mRNA library construction.
RNA libraries were prepared for sequencing using standard BGI-Tech protocols

tag: strain

value: epididymal adipose tissue

value: 8 weeks old


title: RH 013

tag: tissue

value: bone marrow

value: aseptic hip implant loosening


title: WT 1


title: TO Rep4

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

institute: Friedrich Schiller University Jena

description: Library name: sample 16

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Raw sequencing reads were assessed for quality using FastQC (version 0.11.9).
Adaptor trimming, quality filtering, and read preprocessing were performed using fastp (version 0.23.2). In detail, 5' and 3' bases with a Phred quality score below 28 were cut, and reads were removed if they had more than one ambiguous base, an average quality score below 28, or a length of fewer than 15 bases.
Processed reads were aligned to the current A. thaliana genome (tair10.1) using Hisat2 (version 2.2.1) with standard parameters. The aligned reads were sorted and indexed using SAMtools (version 1.11).
Read counting was performed using featureCounts (version 2.0.1) with the tair10.1 annotation as reference.
Assembly: tair10.1
Supplementary files format and content: semicolon-delimited csv file includes raw counts for each sample

source_name: leaves

growth_protocol: 10-day-old seedlings of A. thaliana Col. 0 (A. thaliana) cultivated on MS-medium (Murashige and Skoog, 1962) were transferred to poor nutrient medium (PNM; Camehl et al., 2011) consisting of 5 mM KNO3, 2 mM MgSO4, 2 mM Ca(NO3)2, 0.01 µM FeSO4, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0,2 µM Na2MoO4, 0.01 µM CoCl2, 10.5 g L−1 agar (pH 5.6).

extract_protocol:
RNA was isolated using TRIzol® Reagent (Invitrogen™ by Thermo Fisher Scientific, MA, USA), as described previously (Chomczynski, 1993; Shiko et al., 2023).
RNA sequencing library preparation was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: 7 days old A. thaliana plants were transferred to PNM medium. After 2 days of adaption to the new medium, plants were treated with 10 µM PO (dissolved in 0.12% DMSO) or 10 µM TO, while 0.12% DMSO was used as a mock treatment. Leaves were harvested after 1 h and immediately frozen in liquid nitrogen.

value: leaves

value: 10 µM TO


title: RH 011

tag: cell type

value: mesenchymal stem cells


title: RK 009

value: male


title: PH 004

value: primary

value: coxarthritis


title: TO Rep3

description: Library name: sample 15


title: L-Proline2

first: Kai

last: Huang

address: 168 Changhai Road Shanghai

institute: Changhai hospital

description: Library name: Sample 5

data_processing:
Raw sequencing data in FASTQ format were initially processed using in-house Perl scripts to generate high-quality clean reads. This step involved removing reads containing adapter sequences, reads with poly-N stretches, and low-quality reads. Quality metrics including Q20, Q30 scores and GC content were calculated to assess data integrity. All downstream analyses were performed using these clean reads.
Clean reads were then aligned to the mouse reference genome (GRCm39) using HISAT2 with default parameters. The reference genome file used was: ftp://ftp.ensembl.org/pub/release-109/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz
Gene-level read counts were quantified using HTSeq v0.13.5, based on the corresponding gene annotation file: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.annotation.gtf.gz FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated for each gene using its mapped read count and transcript length, enabling normalization across samples for differential expression analysis.
Assembly: GRCm39
Supplementary files format and content: FPKM for each sample

source_name: heart tissue

growth_protocol: Male C57BL/6J mice (8 weeks old) were housed under standard laboratory conditions (22 ± 2 °C, 12-hour light/dark cycle) with free access to food and water. To induce HFpEF, mice were fed a high-fat diet (HFD) and simultaneously administered L-NAME (0.5 g/L) in drinking water for 8–12 weeks. This combination mimics metabolic stress and nitric oxide deficiency, leading to preserved ejection fraction with diastolic dysfunction—hallmarks of HFpEF.

extract_protocol:
At the study endpoint, left ventricular tissue (~30 mg) was rapidly excised and homogenized in 1 mL of TRIzol reagent (Invitrogen, USA) using a bead mill homogenizer. Total RNA was extracted according to the manufacturer’s instructions. RNA purity and concentration were assessed using a NanoPhotometer spectrophotometer (IMPLEN, CA, USA), and integrity was confirmed by agarose gel electrophoresis or Bioanalyzer analysis to ensure suitability for downstream transcriptomic profiling.
For each sample, 1.5 µg of high-quality total RNA was used to prepare sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA), following the manufacturer’s instructions. Unique index codes were ligated to each library to enable sample multiplexing. After quality assessment and quantification, libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform to generate paired-end reads suitable for transcriptomic analysis.

treatment_protocol: Following HFpEF induction, mice were randomly divided into two groups:HFpEF + PBS (vehicle control) and HFpEF + L-proline (300 mg/kg/day, intraperitoneal injection). L-proline was administered daily for 4–8 weeks to evaluate its role in promoting ferroptosis and exacerbating HFpEF pathology. At the study endpoint, cardiac tissues were harvested for transcriptomic analysis and molecular validation of ferroptosis and PPARγ-related signaling pathways.

value: heart tissue

value: L-proline


title: L-Proline1

description: Library name: Sample 4


title: PBS3

description: Library name: Sample 3

value: PBS


title: PH 003

value: female


title: L-Proline3

description: Library name: Sample 6


title: TO Rep2

description: Library name: sample 14


title: Huh7 cells,mimics-NC,rep1

value: Liver

value: hepatocellular carcinoma cells


title: RK 003

value: revision

value: aseptic knee implant loosening


title: PBS2

description: Library name: Sample 2


title: TO Rep1

description: Library name: sample 13


title: PH 002


title: PBS1

description: Library name: Sample 1


title: KO 2

value: epididymal adipose tissue

tag: age

value: 8 weeks old


title: RK 001

value: bone marrow

tag: Sex


title: CMI WT HTO

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

country: USA

institute: Weill Cornell Medecine

description: Library name: CMI_WT_HTO

library_source: other

data_processing:
Cellranger v3.1.0
Assembly: GRCm38-2020-A
Supplementary files format and content: barcodes.csv, genes.csv, and counts.mtx for RNA
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, and martix.mtx.gz for ADT and HTO
Library strategy: CITE-seq

molecule: protein

source_name: Tumor

growth_protocol: Intradermal tumor implantation

extract_protocol:
Twelve hours after treatment mice were euthanized and tumors were harvested. Samples were then passed through a 100 μm filter and resuspended in 3 ml of 40% Percoll (Fisher Scientific). Samples were then centrifuged at 1500 rpm for 5 minutes. To remove red blood cells, Samples were resuspended in ACK Lysing Buffer (Thermo Fisher) on ice. Cells were then resuspended in FACS Buffer at 1-2 x 106 cells per 100 μL. All wells were treated with DAPI viability dye, washed and then incubated with Fc block. Cells were subsequently pooled according to treatment group. Samples were then sequenced and analyzed.
The single-cell RNA-Seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X Genomics) following the user guide manual for 3′ v3. FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by polymerase chain reaction (PCR) amplification per manual instruction. Samples were multiplexed together on one lane of 10X Chromium. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

treatment_protocol: Intratumoral injection of isotype control or a combination of anti-CD40/MPL/anti-IL-10R (CMI)

value: Tumor

value: Myeloid

value: CMI


title: ISO KO HTO

description: Library name: ISO_KO_HTO

value: ISO


title: PH 001

value: primary

value: mesenchymal stem cells


title: WT 2

tag: genotype


title: PO Rep4

description: Library name: sample 12

value: leaves

tag: treatment

value: 10 µM PO


title: CMI KO HTO

description: Library name: CMI_KO_HTO


title: PO Rep3

description: Library name: sample 11


title: ISO WT HTO

description: Library name: ISO_WT_HTO


title: RK 243

value: male

value: arthrofibrosis; aseptic knee implant loosening


title: CMI KO ADT

description: Library name: CMI_KO_ADT


title: ISO KO ADT

description: Library name: ISO_KO_ADT


title: RK 241

value: female


title: PO Rep2

description: Library name: sample 10


title: CMI WT ADT

description: Library name: CMI_WT_ADT


title: PO Rep1

description: Library name: sample 09


title: CMI KO GEX

description: Library name: CMI_KO_mRNA


title: DMSO Rep4

description: Library name: sample 04


title: RK 228


title: RK 225


title: ISO KO GEX

description: Library name: ISO_KO_mRNA


title: CMI WT GEX

description: Library name: CMI_WT_mRNA


title: ISO WT GEX

description: Library name: ISO_WT_mRNA


title: RK 219


title: DMSO Rep3

description: Library name: sample 03


title: 459-BM_GP1_GEX

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description:
Library name: RS-04318058
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (CR) (v7.0.0) pipeline to generate fastq files. Fastq files were aligned and quantified generating feature-barcode count matrices. Gene-barcode matrices containing Unique Molecular Identifier (UMI) counts are filtered using CR's cell detection algorithm. Processed output obtained from the outs/filtered_feature_bc_matrix folder.
Assembly: Mm10 (10X v2020-A)
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Bone marrow

extract_protocol:
Isolated bone marrow mononuclear cells were processed and re-suspended in PBS+0.04% BSA at a concentration of 1000 cells/uL.
Single-cell transcriptomic libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3' v3.1 chemistry. Prior to library construction, single-cell suspensions were assessed for quality using the ViaStain™ AOPI Staining Solution in combination with a Cellometer K2 automated cell counter (Nexcelom Bioscience) to determine cell concentration, viability, and to confirm the absence of aggregates or debris that might interfere with droplet encapsulation. Cells were loaded onto the Chromium X Controller (10x Genomics), where they were partitioned into nanoliter-scale Gel Beads-in-Emulsion (GEMs), each containing a single cell and a barcoded bead. Within each GEM, reverse transcription was performed to produce uniquely barcoded, full-length cDNA. Following emulsion breakage, the barcoded cDNA was purified and amplified via PCR. Amplified cDNA was enzymatically fragmented, followed by end-repair, A-tailing, adaptor ligation, and sample indexing via PCR to generate Illumina-compatible libraries. The final libraries were assessed for size distribution and integrity using the D1000 ScreenTape assay on a TapeStation 4200 (Agilent Technologies) and quantified using the KAPA Library Quantification Kit for Illumina platforms (Roche). Sequencing libraries were pooled at equimolar concentrations, denatured, and diluted to a final loading concentration of 300 pM with 1% PhiX control library (Illumina). Pooled libraries were sequenced on an Illumina NovaSeq 6000 system, following the manufacturer’s protocol. An average sequencing depth of ~20,000 paired-end reads per cell was achieved for downstream analysis.

treatment_protocol: Our study has 4 treatment groups (Group 1: CAR-T, Group 2: IFNgamma knockout CAR-T and Group 4: CAR-T + Th17). CAR-T or IFNgamma knockout CAR-T cells were administered a week after tumor inoculation (Emu-ALL cells). Th1 (CD4+ T helper cells) and Th17 (CD4+ T helper 17 cells) were admnistered on the same day as CAR-T/ IFNgamma knockout CAR-T treatment. Bone marrow cells were collected at week 4 post treatment for single cell RNA sequencing.

value: Bone marrow

value: Emu-ALL GFP Luciferase

value: Bone marrow mononuclear cells

value: IL-2Ralpha -/- (knockout)

value: CAR-T

tag: group


title: DMSO Rep2

description: Library name: sample 02


title: 418-BM_GP2_GEX

description:
Library name: RS-04318057
10x Genomics

value: IFNgamma knockout CAR-T


title: hth1_H3K4me3_rep2

description: Library name: Sample 31

value: Arabidopsis seedlings

value: Abcam, ab8580

value: hth1-/- (in Col-0)


title: 436-BM_GP2_GEX

description:
Library name: RS-04318056
10x Genomics


title: DMSO Rep1

description: Library name: sample 01


title: 465-BM_GP3_GEX

description:
Library name: RS-04318054
10x Genomics


title: 426-BM_GP1_GEX

description:
Library name: RS-04318055
10x Genomics


title: PH 222

value: bone marrow

value: coxarthritis


title: 446-BM_GP3_GEX

description:
Library name: RS-04318052
10x Genomics


title: PH 215

value: primary

value: mesenchymal stem cells


title: 415-BM_GP4_GEX

description:
Library name: RS-04318053
10x Genomics

value: IFNgamma knockout CAR-T+Th1


title: 416-BM_GP4_GEX

description:
Library name: RS-04318051
10x Genomics


title: ubi-zgli3r,30 hpf, rep8

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description: Library name: Sample 8

data_processing:
paired-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.

organism: Danio rerio

source_name: whole dechorionated embryo, 4 combined

extract_protocol:
RNA extraction, QC, library preparation, and sequencing were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: Total RNA was extracted from frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: whole dechorionated embryo, 4 combined

value: wildtype


title: ISO WT ADT

description: Library name: ISO_WT_ADT

value: Tumor

value: Myeloid

value: ISO


title: ubi-zgli3r,30 hpf, rep7

description: Library name: Sample 7


title: PH 212

value: female


title: TAX2

city: NEW YORK

first: LEVI

last: MANGARIN

address: 413 E 69TH STREET

department: MEYER CANCER CENTER

institute: WEILL CORNELL MEDICINE

description:
Library name: TAX2
10X Chromium v3 scRNAseq FASTQ

data_processing:
Cellranger v3.1.0
Assembly: GRCm38-2020-A
Supplementary files format and content: Tsv and matrix files

source_name: tumor

extract_protocol: 10X Chromium v3 library preparation

value: tumor


title: Ctrl

description:
Library name: Ctrl
10X Chromium v3 scRNAseq FASTQ

value: Ctrl


title: ubi-zgli3r,30 hpf, rep6

description: Library name: Sample 6


title: PH 203


title: PH 006

value: male


title: Intestinal epithelial cells, colon, CARD14(E138A) 3

city: Zwijnaarde

first: Aigerim

last: Aidarova

address: Technologiepark-Zwijnaarde 71

department: Center for Inflammation Research

country: Belgium

institute: VIB-Ghent University

description: Library name: TGcolon-3

data_processing:
Quality control of raw reads was performed using FastQC v0.11.9. Reads showed excellent quality with no adapter contamination. However, base composition at the 5' end differed from the rest of the read, so the first 15 bases were removed during mapping.
Reads were mapped to the mouse reference genome (mm10, Ensembl release 100, April 2020) using HISAT2 v2.1.0 with the parameters: -5 15 (trim first 15 bases), and --rna-strandness R.
Unmapped reads from mouse alignment were retained using --un unmapped.fq and mapped to the human reference genome (hg19, Ensembl release 100) using the same HISAT2 settings to assess CARD14 human transgene expression.
Unmapped reads from mouse alignment were retained using --un unmapped.fq and mapped to the human reference genome (hg19, Ensembl release 100) using the same HISAT2 settings to assess CARD14 human transgene expression.
Mapped reads were converted to sorted BAM files using SAMtools v1.10. Read quantification was performed using featureCounts v2.0.0 with the command: featureCounts -a /annotations/mm10_E100.gtf -o counts.fcnt -T 4 -s 2 *.bam Gene assignment was successful for the majority of reads. Human-mapped reads were quantified similarly using human annotations
Assembly: mm10 (Ensembl release 100) mouse, hg19 (Ensembl release 100) human
Supplementary files format and content: csv file includes raw read counts for each sample

source_name: colon

extract_protocol:
RNA was isolated using an RNeasy Plus micro kit (74134, QIAGEN) according to the manufacturer’s instructions. RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using the Bioanalyzer 2100 (Agilent). Per sample, 250 ng of total RNA was used as input
Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: # 1000000040498 v00 October 2017) Poly-A containing mRNA molecules were purified from total RNA using poly-T oligo-attached magnetic beads. mRNA was then reverse-transcribed into first-strand cDNA using random primers, followed by second-strand synthesis using DNA Polymerase I and RNase H to generate double-stranded cDNA. The cDNA fragments were end-repaired and extended with a single 'A' base at the 3' ends. Indexing adapters were ligated to the cDNA fragments, introducing unique barcodes per sample. Enrichment PCR was performed to amplify adapter-ligated fragments. Libraries were equimolarly pooled and sequenced on an Illumina NovaSeq 6000 using a v1.5 kit, S1 flowcell, and single-end read configuration (100-8-8-0) at the VIB Nucleomics Core https://nucleomicscore.sites.vib.be/

value: colon

value: intestinal epithelial cells


title: Intestinal epithelial cells, colon, CARD14(E138A) 4

description: Library name: TGcolon-4


title: ubi-zgli3r,30 hpf, rep5

description: Library name: Sample 5


title: Hs578T tryptase replicate 2

city: Uppsala

first: Débora

last: Parrine

state: Uppsala

address: Husargatan 3,

department: NBIS

country: Sweden

institute: Scilifelab

description:
Library name: Sample 5
Hs578T trypsin replicate 2

data_processing:
The ATAC-seq analysis was performed using the Nextflow pipeline NF-core/atacseq version 2.1.2 (https://nf-co.re/atacseq). Sequence adapters are trimmed by Trim Galore!, and aligned by BWA
Picard marked duplicates and merged alignments from multiple libraries to one sample, mitochondrial DNA, duplicates, unmapped regions and other unwanted sequences are filtered by SAMtools, Pysam and BAMTools
Normalized bigWig files were generated by BEDTools, and bedGraphToBigWig.
Genome-wide enrichment was done by deepTools and peaks were called by MACS2.
Differential accessibility analysis was performed by DESeq2 and Homer was used to annotate gene features.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: The Hs578T triple-negative human breast cancer cell line (ATCC) was cultured in Dulbecco’s modified Eagle’s medium (Gibco), supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen), 50 mg/ml streptomycin sulfate (Sigma-Aldrich), 60 mg/ml penicillin G (Sigma-Aldrich), 2 mM L-glutamine (SVA, Uppsala, Sweden). Cells were kept at 37°C in 5% CO2 and medium was replaced when cells achieved 90 - 100% confluency

extract_protocol:
Hs578T cells (0.5 x 105 cells) were seeded into wells of a 24-well plate. Triplicates of cells were left untreated or treated with 50 nM recombinant human skin tryptase (Promega) at 37°C for 48 h. Cells were then harvested by centrifugation at 500 x g for 10 min at 4°C and cell pellets were resuspended in 50 μl of cold lysis buffer (10 mM Tris HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40, 0.1 % Tween-20 and 0.01 % digitonin) and incubated on ice for 3 min. Pellets were resuspended with 1 ml wash buffer (10 mM Tris HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % Tween-20) and cell nuclei were pelleted at 500 x g for 10 min at 4°C.
Supernatants were removed and pellets were resuspended in 50 μl of tagmentation master mix (TD buffer, 0.5 % tween 20, 0.5 % digitonin and TDE1 enzyme). Samples were incubated for 30 min at 37°C in a thermomixer 5436 (Eppendorf) with a mixing speed of 1000 rpm, followed by adding 250 μl of ChIP DNA binding buffer to the tagmented DNA. The mixture was transferred to a Zymo-SpinTM IC-XL column in a collection tube, centrifugated for 30 sec at 13,000 x g and the flow-through was discarded. The column was washed twice with 200 μl DNA washing buffer (1 min 13,000 x g) and samples were eluted with 15 μl DNA elution buffer directly to the column matrix (30 sec; 13,000 x g). The eluted DNA samples were transferred to a TwinTec 96-well plate.

treatment_protocol: Cells were left untreated or treated with 50 nM tryptase and incubated at 37°C for 48 h

value: Breast cancer

value: Tryptase


title: Hs578T tryptase replicate 3

description:
Library name: Sample 6
Hs578T trypsin replicate 3


title: ubi-zgli3r,30 hpf, rep4

description: Library name: Sample 4


title: Intestinal epithelial cells, colon, CARD14(E138A) 1

description: Library name: TGcolon-1


title: Hs578T tryptase replicate 1

description:
Library name: Sample 4
Hs578T trypsin replicate 1


title: Intestinal epithelial cells, colon, WT4

description: Library name: WTcolon-4

value: WT


title: ubi-zgli3r,30 hpf, rep3

description: Library name: Sample 3


title: Intestinal epithelial cells, colon, WT3

description: Library name: WTcolon-3


title: WT

description:
Library name: WT
10X Chromium v3 scRNAseq FASTQ

value: Pmel


title: Intestinal epithelial cells, colon, WT2

description: Library name: WTcolon-2


title: Hs578T control replicate 3

description:
Library name: Sample 3
Hs578T control replicate 3


title: HET

description:
Library name: HET
10X Chromium v3 scRNAseq FASTQ

value: HET


title: ubi-zgli3r,30 hpf, rep1

description: Library name: Sample 1


title: Intestinal epithelial cells, small intestine, CARD14(E138A) 4

description: Library name: TGsmallint-4

source_name: small intestine

value: small intestine


title: Hs578T control replicate 2

description:
Library name: Sample 2
Hs578T control replicate 2


title: Intestinal epithelial cells, small intestine, CARD14(E138A) 2

description: Library name: TGsmallint-2


title: ubi-zgli3r,30 hpf, rep2

description: Library name: Sample 2

value: whole dechorionated embryo, 4 combined


title: Intestinal epithelial cells, small intestine, CARD14(E138A) 3

description: Library name: TGsmallint-3


title: Intestinal epithelial cells, colon, CARD14(E138A) 2

description: Library name: TGcolon-2


title: Intestinal epithelial cells, small intestine, WT4

description: Library name: WTsmallint-4


title: Hs578T control replicate 1

description:
Library name: Sample 1
Hs578T control replicate 1


title: Intestinal epithelial cells, colon, WT1

description: Library name: WTcolon-1


title: Cut&Tag_NuGC3-IgG-replication 2

description: Library name: Cut_Tag_NuGC3-IgG-rep2

data_processing:
RNA-seq were filtered by fastp (version 0.20.1). The cleaned reads of RNA-seq were aligned against the hg38 transcriptome using HISAT214 (version 2.1.0) and quantitated with featureCounts. The gene expression were normalized to TPM with our in-house scripts. Low expression genes were filtered and raw count matrix was used for differential expression analysis using edgeR (version 3.28.1). Differential expressed genes (DEGs) were set as FDR < 0.05 and |log2 FoldChange| > 0.58. The clusterProfiler package in R (version 3.6.1) was implemented to perform GO and KEGG pathway enrichment analyses of those DEGs.
The adaptor and low quality bases were removed by using fastp. The clean reads were mapped to human genome hg38 by using bowtie2 with the following parameter ”--end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 2000”. The duplicated reads were removed by using picard. The correlation of replicates were computed and visualized by using deeptools. Then we merged the two replicates of Galectin-3 and EGR1 respectively. Further, peaks were detected by using callpeak method of MACS2 with parameters “-f BAMPE -g hs --nolambda --nomodel --extsize 180 -q 0.05”. The peaks were annotation by using ChIPseeker. The ngs.plot.r was implemented to visualize the distribution of binding signal of Galectin-3 and EGR1. Additionally, Integrative Genomics Viewer (IGV) was implemented to visualize the binding signal of the specific location.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for RNA-seq
Supplementary files format and content: tab-delimited text files include peaks for Cut&Tag
Library strategy: Cut&Tag

value: Human gastric cancer

value: IgG


title: LAPC4 cells, Reawakened conditions, Biol rep 3

city: Tampa

first: Conor

last: Lynch

state: Florida

address: 12902 USF Magnolia Drive

institute: H.Lee MOFFITT Cancer Center

description:
Library name: R-LAPC4_3
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt

data_processing:
The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the P3-200 cycle reagent kit to generate approximately 50M million 100-base read pairs per sample (Illumina, Inc., San Diego, CA). Paired-end sequencing reads were aligned to reference genome GRCh38 or mm10 using STAR v2.5.3a. Gene-level quantification was estimated by RSEM v1.3.0.
Assembly: Gene model GENCODE v30 and vM21 were used for quantification of human and mouse cell lines, respectively.
Supplementary files format and content: Tab delimited text files include raw counts for each species

growth_protocol: RM1 cells were cultured routinely in 10% FBS-supplemented DMEM, while LAPC4 & 22Rv1 were cultured in 10% FBS-supplemented RPMI-1640.

extract_protocol:
RNA was extracted from (RM1, 22Rv1, and LAPC4) under different conditions using RNeasy purification kit (74104, Qiagen) with DNAse treatment (79254, Qiagen). 50 ng was used for library preparation.
The samples were then processed for RNA-sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (NuGEN Technologies, San Carlos, CA).  Briefly, 50 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol.

treatment_protocol:
Dormancy induction was induced by seeding 91,000 cells / cm2 in regular tissue culture plates in serum free DMEM with high glucose (4.5 g/L) and 1% antibiotics for 48 hours.
Reawakening induction was induced by adding 10% FBS-supplemented DMEM to dormant cells for 24 hours.

value: Reawakening induction


title: Cut&Tag_NuGC3-EGR1-replication 2

description: Library name: Cut_Tag_NuGC3-EGR1-rep2


title: Intestinal epithelial cells, small intestine, WT3

description: Library name: WTsmallint-3


title: Intestinal epithelial cells, small intestine, WT1

description: Library name: WTsmallint-1


title: LAPC4 cells, Reawakened conditions, Biol rep 2

description:
Library name: R-LAPC4_2
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Cut&Tag_NuGC3-EGR1-replication 1

description: Library name: Cut_Tag_NuGC3-EGR1-rep1


title: Intestinal epithelial cells, small intestine, WT2

description: Library name: WTsmallint-2


title: Trim66_KO_homo_Olfr1507_OSN_H3K9me3_CUT&Tag_rep_2

first: Yalei

last: Kong

institute: Shanghai Jiao Tong University

description:
Library name: sample 8
H3K9me3_homo_2
Trim66_KO_homo_Olfr1507_OSN_H3K9me3_CUT&Tag_merge_RPM.bw

data_processing:
CUT&Tag: Reads were mapped to the mouse reference genome (mm10) using Bowtie 2 (version 2.5.1) with the “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700” parameters. The olfactory enhancer peaks were visualized in a multi-region track using the UCSC genome browser and deeptools (version 3.5.5).
Hi-C: The In situ Hi-C data were processed following the 4DN Hi-C data processing pipeline (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline). Briefly, sequencing reads were aligned to the mm10 reference genome with BWA (version 0.7.17). Valid Hi-C contacts were extracted by removing PCR duplicates and short cis contacts within 1 kb using pairtools (version 1.0.1) . Hi-C contact matrices were then generated by binning the genome at multiple resolutions and normalized using matrix balancing implemented in cooler (version 0.9.2). To account for variations in sequencing depth and alignment efficiency, contact frequencies were normalized by dividing the binned interaction counts by the total number of Hi-C contacts at the specified resolution. Contact matrices were visualized using Python libraries including pandas, seaborn, and matplotlib. Aggregate pileup analyses were conducted using the pileup function from the coolpuppy package (version 1.1.0). A/B compartment profiles were derived from ICE-normalized intrachromosomal contact maps at 500 kb resolution by converting them into observed-over-expected (O/E) matrices. Principal component analysis (PCA) was performed, and PC1 values were interpreted based on GC content. Regions with positive PC1 scores, typically gene-rich, were assigned as compartment A, while regions with negative PC1 scores were assigned  as compartment B. Compartment strength was assessed and visualized by saddle plots in cooltools (version 0.5.4). TADs were identified by calculating insulation scores via the diamond insulation algorithm implemented in cooltools, with a window size of 125 kb and a bin size of 25 kb.
Assembly: mm10
Supplementary files format and content: CUT&Tag: bigWig files
Supplementary files format and content: Hi-C: mcool files
Library strategy: CUT&Tag

source_name: Main Olfactory Epithelium (MOE)

extract_protocol:
CUT&Tag: The MOE from Olfr1507-ires-tdTomato; Trim66 -/- or Olfr1507-ires-tdTomato; Trim66 +/- mice was dissected and dissociated. Then more than 10,000 tdTomato-positive cells were sorted by flow cytometry
CUT&Tag: Libraries were prepared with the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).
Hi-C: The MOE from Trim66 -/- or Trim66 +/- mice was dissected and dissociated.
Hi-C: The live cells were fixed with 1% formaldehyde for 10 min and quenched with 0.2 M glycine for 5 min at room temperature. The cells were then washed twice with 100 μL HBSS containing 0.1% BSA. The pelleted cells were resuspended in 100 μL of ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630, and protease inhibitors) and incubated on ice for 30 min. After centrifugation at 3,000 g for 5 min at 4 °C, the pelleted nuclei were washed once with 100 μL of ice-cold 1 NEB Buffer 3.1. Chromatin was solubilized in 20 μL of 0.3% SDS and incubated at 65 °C for 10 min, followed by quenching with 5 μL of 10% Triton X-100 and incubation at 37 °C for 10 min. The nuclei were digested with 50 U DpnII in a total volume of 50 μL at 37 °C for 3 h in a Thermomixer with interval shaking. DpnII was then inactivated by incubation at 65 °C for 20 min. For biotin labeling, 3 μL of 1 mM biotin-14-dATP, 0.3 μL of 10 mM dGTP, 0.3 μL of 10 mM dTTP, 0.3 μL of 10 mM dCTP, and 10 U Klenow were added. The reaction was performed at 37 °C for 1.5 h in a Thermomixer. Subsequently, 60 μL of ligation mixture (33.6 μL water, 12 μL 10 NEB T4 DNA ligase buffer, 12 μL 10% Triton X-100, 1.2 μL 10 mg/mL BSA, and 1.2 μL 2,000 U/μL T4 DNA ligase) was added, and the reaction was incubated at 25 °C for 4 h in a Thermomixer. Crosslinks were reversed and DNA was purified. The purified DNA was sheared to 300–500 bp using a Covaris M220. End repair, dA-tailing, and adaptor ligation were then performed using the Rapid Plus DNA Lib Prep Kit V2 (ABclonal). Biotin-labeled DNA fragments were enriched using 50 μL of Dynabeads MyOne Streptavidin C1 (Invitrogen). Sequencing libraries were prepared on beads, followed by 6–8 cycles of PCR amplification. Fragments ranging from 300 bp to 1,000 bp were size-selected. All libraries were sequenced on a NovaSeq X Plus platform following the manufacturer’s instructions.

value: Main Olfactory Epithelium (MOE)


title: Cut&Tag_NuGC3-IgG-replication 1

description: Library name: Cut_Tag_NuGC3-IgG-rep1


title: Trim66_KO_homo_Olfr1507_OSN_H3K9me3_CUT&Tag_rep_1

description:
Library name: sample 7
H3K9me3_homo_1
Trim66_KO_homo_Olfr1507_OSN_H3K9me3_CUT&Tag_merge_RPM.bw


title: Trim66_KO_het_Olfr1507_OSN_H3K9me3_CUT&Tag_rep_1

description:
Library name: sample 5
H3K9me3_het_1
Trim66_KO_het_Olfr1507_OSN_H3K9me3_CUT&Tag_merge_RPM.bw


title: Trim66_KO_het_Olfr1507_OSN_H3K9me3_CUT&Tag_rep_2

description:
Library name: sample 6
H3K9me3_het_2
Trim66_KO_het_Olfr1507_OSN_H3K9me3_CUT&Tag_merge_RPM.bw


title: Trim66_KO_homo_Olfr1507_OSN_H3K4me1_CUT&Tag_rep_2

description:
Library name: sample 4
H3K4me1_homo_2
Trim66_KO_homo_Olfr1507_OSN_H3K4me1_CUT&Tag_merge_RPM.bw


title: LAPC4 cells, Reawakened conditions, Biol rep 1

description:
Library name: R-LAPC4_1
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Cut&Tag_NuGC3-Gac3-replication 2

description: Library name: Cut_Tag_NuGC3-Gac3-rep2


title: Cut&Tag_NuGC3-Gac3-replication 1

description: Library name: Cut_Tag_NuGC3-Gac3-rep1


title: LAPC4 cells, Dormant conditions, Biol rep 2

description:
Library name: D-LAPC4_2
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt

value: Dormancy induction


title: Trim66_KO_homo_Olfr1507_OSN_H3K4me1_CUT&Tag_rep_1

description:
Library name: sample 3
H3K4me1_homo_1
Trim66_KO_homo_Olfr1507_OSN_H3K4me1_CUT&Tag_merge_RPM.bw


title: Intestinal epithelial cells, small intestine, CARD14(E138A) 1

description: Library name: TGsmallint-1


title: Trim66_KO_het_Olfr1507_OSN_H3K4me1_CUT&Tag_rep_1

description:
Library name: sample 1
H3K4me1_het_1
Trim66_KO_het_Olfr1507_OSN_H3K4me1_CUT&Tag_merge_RPM.bw


title: LAPC4 cells, Dormant conditions, Biol rep 1

description:
Library name: D-LAPC4_1
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Nf2-/- (Nf2), mouse 1048, female

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

description:
Library name: Sample 11
1048-NF2F

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome avaiable on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
The hit counts were summarized and reported using the geneID feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38
Supplementary files format and content: raw counts as comma separated values files "raw_counts.csv" where column header is "X-mouse #-genotype-sex"

source_name: dorsal root ganglion

growth_protocol: Dorsal root ganglia (8 per mouse) tissue was microdissected from 10-month old euthanized Postn-Cre(+);Nf2 flox/flox animals (n=6, 3 male, 3 female) and from Postn-Cre(+);Nf2 flox/flox;Fak1 flox/flox (double knockout, DKO) animals(n=6, 3 male, 3 female), flash frozen and sent to Azenta/GenWiz for mRNA sequencing.

extract_protocol:
Performed by Azenta/GeneWiz: Qiagen Rneasy Plus Mini Kit with DNase treatment
NEBNext Ultra II RNA Library Prep with PolyA selection, 500ng input, 10 PCR amplification cycles

value: dorsal root ganglion

value: female


title: Trim66_KO_het_Olfr1507_OSN_H3K4me1_CUT&Tag_rep_2

description:
Library name: sample 2
H3K4me1_het_1
Trim66_KO_het_Olfr1507_OSN_H3K4me1_CUT&Tag_merge_RPM.bw


title: Nf2-/- (Nf2), mouse 1049, female

description:
Library name: Sample 12
1049-NF2F


title: WD-CCl4 + Vehicle_WD-DEN + EVT0185_WD-DEN + Vehicle

city: Hamilton

first: DONGDONG

last: WANG

state: Ontario

address: 1200 Main Street West

country: Canada

institute: McMaster University

description:
Library name: CCl4_V_45_DEN_T_516
Sample was demultiplexed from Pool 4

data_processing:
Raw FASTQ files from each of the four pooled libraries were processed using the 10X Genomics Cell Ranger multi pipeline (v8.0.0) to demultiplex samples and generate gene expression matrices. Demultiplexing was performed based on sample-specific barcodes introduced during probe hybridization. The following parameters were used: --transcriptome=mm10-2020-A, --probe-set=Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1, and --force-cells=6000.
Assembly: mm10-2020-A
Supplementary files format and content: Sample-specific gene-by-cell expression matrices provided in HDF5 (.h5) format for each of the 12 study samples.

source_name: liver

extract_protocol:
Snap-frozen liver tissue (~20mg) from each mouse was used to generate fixed single-cell suspensions using an optimized version of the 10X Genomics “Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling” protocol (CG000553, Rev B). Fixation was performed using methanol-free formaldehyde, followed by mechanical and enzymatic dissociation with Liberase TH (thermolysin high). Dissociation conditions were optimized to improve yield and quality, including increasing enzyme concentration and extending incubation time to 1 hour. Final cell suspensions were stained with propidium iodide and counted via fluorescence microscopy to ensure high-quality single-cell input.
Library construction was performed using the 10X Genomics Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples, following the manufacturer’s user guide (CG000527, Rev D) without deviation. Briefly, this included sample-specific probe hybridization and barcoding, multiplexing of samples across four pooled libraries, GEM generation, gel bead dissolution and cell lysis, GEM recovery, cDNA pre-amplification, and final library construction. All four libraries passed QC and were used for downstream sequencing. Libraries were constructed to target approximately 6,000 cells per sample at a depth of 25,000 read pairs per cell, as recommended for detecting low-abundance hepatic cell types.

value: liver

tag: mouse line

value: M

tag: diet

value: WD (Envigo, Teklad Custom Research Diet., Madison, WI. Cat# TD.120528) + Glucose/Fructose sugar water_WD (Research Diets, Inc., Code:D19101102)

tag: housing condition

tag: injection condition

value: CCl4, 0.2 µL/g bw, weekly IP_DEN, 25 mg/kg bw, once at 2wk

tag: gavage condition

value: EVT0185 (100mg/kg)_Vehicle (1.5 % CMC and 0.2 % Tween-20)


title: WD-CCl4 + EVT0185_WD-CCl4 + Vehicle

description:
Library name: CCl4_T_83_CCl4_V_67_DEN_V_508
Sample was demultiplexed from Pool 2


title: Nf2-/- (Nf2), mouse 918, female

description:
Library name: Sample 10
918-NF2F


title: WD-CCl4 + EVT0185_WD-CCl4 + Vehicle_WD-DEN + EVT0185

description:
Library name: CCl4_T_4_CCl4_V_66_DEN_T_483
Sample was demultiplexed from Pool 3


title: Nf2-/-;Fak1-/- (DKO), mouse 917, male

description:
Library name: Sample 9
917-DKOM

value: male


title: WD-CCl4_DEN + EVT0185_WD-DEN + Vehicle_WD-DEN + Vehicle

description:
Library name: CCl4_T_1_DEN_T_470_DEN_V_451
Sample was demultiplexed from Pool 1


title: LAPC4 cells, Active conditions, Biol rep 1

description:
Library name: LAPC4_1
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt

tag: cell line


title: LAPC4 cells, Dormant conditions, Biol rep 3

description:
Library name: D-LAPC4_3
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Nf2-/-;Fak1-/- (DKO), mouse 914, male

description:
Library name: Sample 7
914-DKOM


title: sc2_Experiment3_WT1

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description:
Library name: Sample 11
Experiment3_WT1

data_processing:
The raw sequence data were processed using Cell Ranger software (version: 4.0.0). The reads were aligned to mouse genome mm10 and gene counts matrix was summarized for each sample.
Assembly: mm10
Supplementary files format and content: HDF5 of the raw counts

source_name: Breast

extract_protocol:
E0771.lmb tumors were grown after tamoxifen injection as previously described in wild-type and Cdh5-creERt2/Shb flox/flox mice. Mice were sacrificed on day 14-16 after tumor cell injection. The tumors were digested, CD45+-cells isolated by MACS microbeads (Miltenyi, Bergich Gladbach, Germany)
Sequencing libraries were prepared from 10 000 cells after recovery using the Chromium Next GEM Single Cell 3’ Reagent kit v3.1 with dual-index (cat# 1000268/269/120/127/1000215, 10x Genomics) according to the manufacturer’ protocol (User guide CG000315, Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), 10x Genomics).

value: Breast

value: adult

value: WT


title: 22Rv1 cells, Reawakened conditions, Biol rep 3

description:
Library name: R-22RV1_3
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: sc2_Experiment3_KO2

description:
Library name: Sample 10
Experiment3_KO2

value: KO


title: sc2_Experiment3_KO1

description:
Library name: Sample 9
Experiment3_KO1


title: sc2_Experiment2_WT2

description:
Library name: Sample 8
Experiment2_WT2


title: sc2_Experiment2_WT1

description:
Library name: Sample 7
Experiment2_WT1


title: sc2_Experiment2_KO2

description:
Library name: Sample 6
Experiment2_KO2


title: Nf2-/-;Fak1-/- (DKO), mouse 887, female

description:
Library name: Sample 6
887-DKOF


title: sc2_Experiment2_KO1

description:
Library name: Sample 5
Experiment2_KO1


title: 22Rv1 cells, Reawakened conditions, Biol rep 1

description:
Library name: R-22RV1_1
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: LAPC4 cells, Active conditions, Biol rep 3

description:
Library name: LAPC4_3
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: sc2_Experiment1_WT2

description:
Library name: Sample 4
Experiment1_WT2


title: sc2_Experiment1_KO2

description:
Library name: Sample 2
Experiment1_KO2


title: sc2_Experiment1_WT1

description:
Library name: Sample 3
Experiment1_WT1


title: Nf2-/-;Fak1-/- (DKO), mouse 885, female

description:
Library name: Sample 4
885-DKOF


title: 22Rv1 cells, Dormant conditions, Biol rep 3

description:
Library name: D-22RV1_3
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Nf2-/-;Fak1-/- (DKO), mouse 886, female

description:
Library name: Sample 5
886-DKOF


title: 22Rv1 cells, Dormant conditions, Biol rep 2

description:
Library name: D-22RV1_2
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Nf2-/-;Fak1-/- (DKO), mouse 915, male

description:
Library name: Sample 8
915-DKOM


title: Nf2-/- (Nf2), mouse 884, male

description:
Library name: Sample 3
884-NF2M


title: LAPC4 cells, Active conditions, Biol rep 2

description:
Library name: LAPC4_2
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: 22Rv1 cells, Dormant conditions, Biol rep 1

description:
Library name: D-22RV1_1
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: Nf2-/- (Nf2), mouse 702, male

description:
Library name: Sample 2
702-NF2M


title: sc1_Experiment2_WT1

description:
Library name: Sample 7
Experiment2_WT1

extract_protocol:
E0771.lmb tumors were grown  as previously described in wild-type and Shb ICKO (Shb flox/flox; Vav1-cre) mice. Mice were sacrificed on day 14-16 after tumor cell injection and CD45+ cells isolated by MACS microbeads.
Sequencing libraries were prepared from 10 000 cells after recovery using the Chromium Next GEM Single Cell 3’ Reagent kit v3.1 with dual-index (cat# 1000268/269/120/127/1000215, 10x Genomics) according to the manufacturer’ protocol (User guide CG000315, Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), 10x Genomics).


title: sc1_Experiment2_WT2

description:
Library name: Sample 8
Experiment2_WT2


title: sc1_Experiment2_KO2

description:
Library name: Sample 6
Experiment2_KO2


title: sc1_Experiment2_KO1

description:
Library name: Sample 5
Experiment2_KO1


title: Nf2-/- (Nf2), mouse 649, male

description:
Library name: Sample 1
649-NF2M


title: sc1_Experiment1_WT2

description:
Library name: Sample 4
Experiment1_WT2


title: 22Rv1 cells, Active conditions, Biol rep 2

description:
Library name: 22RV1_D2_2
Lynch_LAPC4_22RV1_Human_rsem_raw_count.txt


title: sc1_Experiment1_WT1

description:
Library name: Sample 3
Experiment1_WT1