title: Cfpac1 cells, ChIPseq H3K27ac, Trametinib 12h, Rep1


title: AY00945

status: Public on Feb 19 2024

type: RNA

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

description: Sample 19

hyb_protocol: Per manufacturer protocols.

scan_protocol: Scanning was performed on the NanoString nCounter platform per the manufacturer protocols.

data_processing: All data analysis used Bioconductor version 3.14 or 3.16 packages in R version 4.1 or 4.2, respectively, unless otherwise stated. Raw NanoString data (RCC files) was processed using the NanoStringQCPro package (v1.26.0). For quality control, the geometric mean of the housekeeping genes was used as a metric of overall RNA quality and quantity, and samples with a value of < 100 were excluded. The data from all samples was normalized together using housekeeping genes and positive control genes as recommended in the NanoString data analysis guidelines. Briefly, for each sample a normalization was performed sequentially using first the positive controls and then the housekeeping genes. For each sample the geometric mean of the positive controls was calculated (geomeancontrol). The geometric mean of all the geometric means was then calculated (geomeangeomeans) and this was used to calculate a sample specific normalization factor (geomeangeomeans /geomeancontrol), which was multiplied by the gene counts for each sample. The same steps were then taken using the housekeeping genes instead of the positive controls, to provide the final normalized gene counts.

molecule: total RNA

organism: Homo sapiens

source_name: pediatric brain tumor

label_protocol: Gene quantification was performed on the NanoString nCounter platform per the manufacturer protocols.

extract_protocol: Total RNA was extracted from FFPE and snap frozen tissue using RNAstorm FFPE and fresh frozen kits, respectively, as per the manufacturer's instructions (CellData). RNA concentration was measured (Nanodrop) and RNA integrity assessed using the Agilent 2100 bioanalyzer.

tag: tumor type

value: LGG

tag: nanostring cartridge


title: WT-HuR Input rep2

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description:
Human hepatoma HuH-7 cell line stably overexpressing WT HuR.
Stranded Total RNA-seq

library_source: transcriptomic

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) software was used to generate gene counts.
Genome_build: human genome hg19
Supplementary_files_format_and_content: Text files containing gene counts.

source_name: cultured hepatoma cells

growth_protocol: Human hepatoma HuH-7 cells were grown in the medium stated in the manufacturer’s instructions. All cell lines were maintained in culture for a maximum of 20 passages in a humidified incubator at 37ºC and 5% CO2.

extract_protocol:
RNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol and precipitated overnight in the presence of 100% ethanol, sodium acetate 3 M pH 5.5 and GlycoBlue Coprecipitant. The RNA pellet was washed with 70% ethanol, air dried and resuspended in H2O.
The quantity and quality of the RNAs were evaluated using Agilent RNA 6000 Pico Chips (5067-1513, Agilent Technologies). 16-77 ng of RNA from each RIP sample and 250 ng of RNA from each input sample was used for RNA-seq library preparation. Sequencing libraries were prepared using the TruSeq Stranded Total RNA Human/Mouse/Rat kit (RS-122-2201, Illumina Inc.), following the manufacturer’s guidelines.

tag: cell line

tag: genotype

value: HuR wild type overexpression


title: Cfpac1 cells, ChIPseq H3K27ac, Trametinib 3h, Rep1

city: Milan

first: Serena

last: Ghisletti

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

library_source: genomic

data_processing:
Reads were processed using Trimmomatic v0.39. Next, high-quality trimmed reads were aligned onto the human genome build GRCh38/hg38 using Shortstack v3.8.5 (PMID 23610128) with the following settings: --mismatches 2 --bowtie_m 100 --align_only --mmap u. Mapped reads were filtered to remove randomly placed multi-mappers and unmapped reads using samtools v1.16.9. Any alignment matching hg38-blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz) was discarded using bedtools_v.2.30.0 (PMID 20110278) and duplicate reads removed with the samtools ‘markdup –r’ option. For the H3k27ac ChIP data, peaks were called using MACS2 v.2.2.7.1 (PMID 18798982) with the following parameters: --nomodel –extsize 250 –mfold 5 50 –broad –broad-cutoff 0.01. For the ELF3 ChIP data, we run MACS in ‘narrow-peak’ mode with parameters –nomodel –extsize 200 --mfold 5 50 -q 0.01.  H3K9me3 islands were called using Sicer2 v1.0.3 (PMID 19505939) with the following settings: --window_size=200 –fragment_size=300 -fdr=0.01 –gap_size=600. A corresponding input DNA from the same cell line was used as a control in peak detection in each data set.
Fragment pile-up in ‘Read Per Million’ were generated using MACS2 callpeak with parameters –format BAM –nomodel –B –SPMR, with the –extsize parameter set as the same used in the calling step. The resulting BedGraph files from ChIP was compared to that of the input to generate a signal profile in for data visualization in the genome browser (BigWig files).
Assembly: GRCh38 assembly version
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

molecule: genomic DNA

growth_protocol: Cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM) +10% fetal bovine serum (FBS) (CFPAC-1), RPMI+15% FBS (CAPAN-2), Dulbecco's Modified Eagle Medium+10% FBS (MiaPaca-2, PANC-1, HEK293T). Media were all supplemented with 2 mM L-glutamine.

extract_protocol:
ChIP-seq was carried out as previously described (PMID 32997974) using 1x106 cells for the H3K27ac and H3K9me3 ChIP and 20×106 cells for the ELF3 ChIP. The following antibodies were used:  anti-H3K27ac (Abcam, ab4729), anti-H3K9me3 (Abcam, ab8898) and anti-ELF3 antibody (rabbit polyclonal antibody generated in-house using a peptide corresponding to aa1-150 of the human ELF3 reference protein sequence). DNA libraries were prepared as described (PMID 29706544) and sequenced on Illumina NextSeq 500 and NovaSeq6000 platforms.
All ChIPseq data sets were processed in single-end.

treatment_protocol: Trametinib (Selleckchem S2673) was diluted in DMSO and used at a concentration of 20 nM for all the experiments. Cells were plated in 96 well, 24 well, 6 well or 10 cm plates 24-48 h before treatment and treated for the indicated time at the reported concentration of drugs directly diluted in their own medium

tag: cell type

value: PDAC Low-Grade

value: Wild type

tag: treatment

value: Trametinib 3h

tag: chip antibody


title: WT-HuR Input rep1


title: C2C12_D96_RNAseq_rep2

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

description:
C2C12, 96 hours after differentiation, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads, TGS raw data gained from MinION nanopore with single end reads
For Illumina sequencing data, Cutadapt (v2.8) (Martin, 2011) was firstly used to cut the sequencing adapters of the paired-end reads with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGT -m 15 -e 0.15. The NAP-seq specific 5’-adapter (AAGCAGTGGTATCAACGCAGAGT) and 3’-adapter (AGTCGTAGTAAGTCTGTGCTCG) which marked the boundary of the napRNAs were subsequently moved by our programme flClipAdapter with the following parameters: -l 15 -e 0.1 -c 6. Finally, the reads were mapped to the reference genome (hg38 or mm10) with STAR (Dobin et al., 2013) software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20  --outFilterMatchNminOverLread 0.8  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat .     For nanopore sequencing data, Cutadapt (v2.8) was used to cut the NAP-seq specific adapters with the following parameters: -j 16 -g AAGCAGTGGTATCAACGCAGAGT -a AGTCGTAGTAAGTCTGTGCTCG -m 20 -e 0.3 -O 10, and then use Cutadapt again to move any possible adapters with the following parameters: -j 16 -g CGAGCACAGACTTACTACGACT -a ACTCTGCGTTGATACCACTGCTT -m 20 -e 0.3 -O 10, and we just retained the read that contained the NAP-seq specific adapters. Finally, thr reads were mapped to the reference genome (hg38) with minimap2 (Li, 2018) with the following parameters: --junc-bed hg38.gencode.v30.geneAnno.bed -t 16 -k15 -w5 --splice -g2000 -G200k -A2 -B4 -O4,96 -E2,0 -C18 -z400,200 -ub --end-bonus=18 --junc-bonus=18 --splice-flank=yes -ub --sam-hit-only --secondary=no -a    For SHAPE-MaP data, preprocessing of SHAPE-MaP sequencing data was the same as NAP-seq Illumina sequencing data, including remove the sequencing adapters and NAP-seq specific adapters. Then clean paired-end reads of three biological replicates were merge and mapped to each identified napRNAs. The alignments for individual napRNAs were extracted and processed with shapemapper_mutation_parser, shapemapper_mutation_counter and the python script make_reactivity_profiles.py from ShapeMapper2 to produce the reactivity profiles. The SHAPE reactivity profiles were used to guide RNA structure prediction using RNA RNAalifold. We further manually adjust the RNA structure for some polyA-pocket-ACA-napRNAs to make it more more consistent to the hairpin-pocket-hinge-hairpin structure.    For CAP-seq data, Cutadapt (v2.8) (Martin, 2011) was first used with the following parameters to remove the sequencing adapters from the paired-end reads: cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 3 -e 0.15. Then the reads were mapped to the reference genome (hg38) with STAR (Dobin et al., 2013) software.
To identify pronounced high-confidence napRNAs, we firstly assembled the continuous reads to the contigs, and then calculated the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We reasoned that the startReadNum and endReadNum of a candidate napRNA should be significantly higher over the sequence upstream and downstream, while the coverage of the contigs should also be significantly higher over the regions around.  Finally, we developed the computational software napSeeker to calculate the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We calculated the fold change between startReadNum and numbers of reads containing specific 5’-adapter within 100nt upstream and downstream (startFC), in a similar way, the fold change between endReadNum and the numbers of reads containing specific 3’-adapter upstream and downstream within 100nt (endFC). Next, we calculated the fold change between coverage of the contigs and the regions within 20nt upstream/downstream (up20ntFC/down20ntFC).  A high-confidence napRNA had to meet the following criteria: (1) startReadNum, endReadNum ≥ 7; (2) startFold, endFold ≥ 2. (2) up20ntFold, down20ntFold ≥ 2. (4) length≥100. What’s more, the candidate napRNAs had to express in at least 2 samples of all the human (or mouse) samples. Finally, we only retained the napRNA with the summary counts ≥ 20. These stringent parameters allowed us to identify the highest-confidence candidate napRNAs.  To identify the highest-confidence candidate 5’-Cap sites, we calculated the 5’-end sites coverage of the sequencing read (endCov), the one nucleotide upstream (upCov) and the one nucleotide downstream (downCov). A positive 5’-Cap sites had to meet the following criteria: (1) upFC = endCov/upCov≥2; (2) downFC = endCov/downCov≥2; (3) read counts≥10; (4) P-value<0.05; (5) existing in two replicates; (6) located within mRNA 5`UTR region.
Assembly: hg38, mm10
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: mouse myoblast cells

growth_protocol: HepG2 and U-87 MG were cultured in MEM supplemented with 10% FBS, 1% penicillin-streptomycin at 37 °C in a humidified. HEK293T and C2C12 cells were clutured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 95% air and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. 2ug total RNA was used to prepare the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina or nanopore protocols

treatment_protocol: HepG2 cells were treated with 500ng/ml ADR or 500μM CoCl2 for 24h before harvesting; 2ug/ml poly (I:C) were transfected into HepG2 with lipo2000 and then the cells were cultured for 12h before harvesting. C2C12 cells grow up to 80% confluence, and then the culture medium was changed to the differentiation medium which is consisted of DMEM with 2% horse serum.

value: 96 hours after differentiation

value: wild type


title: C2C12_D96_RNAseq_rep3

description:
C2C12, 96 hours after differentiation, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: AY00943

description: Sample 18

value: HGG


title: AY00940

description: Sample 17


title: Cfpac1 cells, ChIPseq H3K27ac, Trametinib 3h, Rep2


title: HuR [K120/182R] RIP rep2

description:
Human hepatoma HuH-7 cell line stably expressing HuR(K120/182R) SUMOylation mutant.
Stranded Total RNA-seq
RNA bound to V5-tagged HuR.

value: HuR [K120/182R] mutant expression


title: HuR [K120/182R] RIP rep3


title: C2C12_D72_RNAseq_rep3

description:
C2C12, 72 hours after differentiation, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

value: 72 hours after differentiation


title: Cfpac1 cells, ChIPseq H3K27ac, Untreated, Rep1

value: Untreated


title: AY00930

description: Sample 15


title: HuR [K120/182R] RIP rep1


title: WT-HuR RIP rep3

description:
Human hepatoma HuH-7 cell line stably overexpressing WT HuR.
Stranded Total RNA-seq
RNA bound to V5-tagged HuR.


title: AY00925

description: Sample 14


title: C2C12_D96_RNAseq_rep1

description:
C2C12, 96 hours after differentiation, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: Capan2 cells, ChIPseq H3K27ac, Trametinib 24h, Rep2

value: Trametinib 24h


title: WT-HuR RIP rep2


title: Cfpac1 cells, ChIPseq H3K27ac, Untreated, Rep2


title: C2C12_D72_RNAseq_rep1

description:
C2C12, 72 hours after differentiation, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: Capan2 cells, ChIPseq H3K27ac, Trametinib 24h, Rep1


title: C2C12_D72_RNAseq_rep2

description:
C2C12, 72 hours after differentiation, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: C2C12_D0_RNAseq_rep3

description:
C2C12, 0 hours after differentiation, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

value: 0 hours after differentiation


title: Capan2 cells, ChIPseq H3K27ac, Trametinib 12h, Rep2

value: Trametinib 12h


title: WT-HuR RIP rep1


title: AY00918

description: Sample 12


title: AY00934

description: Sample 16


title: C2C12_D0_RNAseq_rep2

description:
C2C12, 0 hours after differentiation, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: rnc_GDSR_phototroph_3

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description: Rhodobacter sphaeroides rnc mutant grown under phototrophic conditions, rep 3

data_processing:
Alignment of FASTQ files against the Cereibacter sphaeroides 2.4.1 genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) was performed using the READemption v.1.0.5.
Read counts per gene were calculated using the summarizedOverlaps.
DESeq2 v.1.32 was used for the normalization of the reads and the identification of transcriptional changes.
Additionally, bona fide RNase III cleavage sites were identified.
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: wiggle format containing the total read coverage merged from the biological triplicates

organism: Cereibacter sphaeroides

source_name: rnc_GD48,49SR (rnc-)

growth_protocol: Cells were grown in malate minimal medium, either in presence of high oxygen concentration of 180 µM dissolved oxygen (aerobic cultures), low oxygen concentration of 25 µM dissolved oxygen (microaerobic cultures) or without oxygen but illuminated with 60 W*m-2 white light (phototrophic cultures).

extract_protocol:
Total RNA was isolated as published (Grützner et al., 2021, Nucelic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set

treatment_protocol: Cells were harvested during exponential growth phase.

value: rnc_GD48,49SR (rnc-)


title: Capan2 cells, ChIPseq H3K27ac, Trametinib 3h, Rep2


title: C2C12_D0_RNAseq_rep1

description:
C2C12, 0 hours after differentiation, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: AY00915

description: Sample 10


title: Capan2 cells, ChIPseq H3K27ac, Trametinib 12h, Rep1


title: rnc_GDSR_phototroph_2

description: Rhodobacter sphaeroides rnc mutant grown under phototrophic conditions, rep 2


title: C2C12, 144 hours after differentiation, biological replicate3

description: Discover the full-length non-capped RNAs of the mammalian transcriptome

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads, TGS raw data gained from MinION nanopore with single end reads
For Illumina sequencing data, Cutadapt (v2.8) (Martin, 2011) was firstly used to cut the sequencing adapters of the paired-end reads with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGT -m 15 -e 0.15. The NAP-seq specific 5’-adapter (AAGCAGTGGTATCAACGCAGAGT) and 3’-adapter (AGTCGTAGTAAGTCTGTGCTCG) which marked the boundary of the napRNAs were subsequently moved by our programme flClipAdapter with the following parameters: -l 15 -e 0.1 -c 6. Finally, the reads were mapped to the reference genome (hg38 or mm10) with STAR (Dobin et al., 2013) software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20  --outFilterMatchNminOverLread 0.8  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat .   For nanopore sequencing data, Cutadapt (v2.8) was used to cut the NAP-seq specific adapters with the following parameters: -j 16 -g AAGCAGTGGTATCAACGCAGAGT -a AGTCGTAGTAAGTCTGTGCTCG -m 20 -e 0.3 -O 10, and then use Cutadapt again to move any possible adapters with the following parameters: -j 16 -g CGAGCACAGACTTACTACGACT -a ACTCTGCGTTGATACCACTGCTT -m 20 -e 0.3 -O 10, and we just retained the read that contained the NAP-seq specific adapters. Finally, thr reads were mapped to the reference genome (hg38) with minimap2 (Li, 2018) with the following parameters: --junc-bed hg38.gencode.v30.geneAnno.bed -t 16 -k15 -w5 --splice -g2000 -G200k -A2 -B4 -O4,96 -E2,0 -C18 -z400,200 -ub --end-bonus=18 --junc-bonus=18 --splice-flank=yes -ub --sam-hit-only --secondary=no -a
To identify pronounced high-confidence napRNAs, we firstly assembled the continuous reads to the contigs, and then calculated the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We reasoned that the startReadNum and endReadNum of a candidate napRNA should be significantly higher over the sequence upstream and downstream, while the coverage of the contigs should also be significantly higher over the regions around.  Finally, we developed the computational software napSeeker to calculate the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We calculated the fold change between startReadNum and numbers of reads containing specific 5’-adapter within 100nt upstream and downstream (startFC), in a similar way, the fold change between endReadNum and the numbers of reads containing specific 3’-adapter upstream and downstream within 100nt (endFC). Next, we calculated the fold change between coverage of the contigs and the regions within 20nt upstream/downstream (up20ntFC/down20ntFC).  A high-confidence napRNA had to meet the following criteria: (1) startReadNum, endReadNum ≥ 7; (2) startFold, endFold ≥ 2. (2) up20ntFold, down20ntFold ≥ 2. (4) length≥100. What’s more, the candidate napRNAs had to express in at least 2 samples of all the human (or mouse) samples. Finally, we only retained the napRNA with the summary counts ≥ 20. These stringent parameters allowed us to identify the highest-confidence candidate napRNAs.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (RPM).

value: 144 hours after differentiation

tag: treatment label

tag: molecule subtype

value: total RNA, remove rRNA


title: AY00917

description: Sample 11


title: AY00913

description: Sample 9

value: LGG


title: Capan2 cells, ChIPseq H3K27ac, Trametinib 3h, Rep1


title: AY00921

description: Sample 13


title: AY00909

description: Sample 8


title: Capan2 cells, ChIPseq H3K27ac, Untreated, Rep2


title: C2C12, 144 hours after differentiation, biological replicate1


title: AY00906

description: Sample 6


title: rnc_GDSR_microaerob_2

description: Rhodobacter sphaeroides rnc mutant grown under microaerobic conditions, rep 2


title: C2C12, 96 hours after differentiation, biological replicate3


title: SEZ, middle-aged, H, snRNA-seq

city: Nijmegen

first: Sofia

last: Puvogel

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: RadboudUMC

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed and aligned to the GRCh38 human genome using CellRanger v3.0.1
Filtered count matrices generated by Cell Ranger were loaded in R v4.0 with Seurat v4.0.
Nuclei with mitochondrial content > 5% were removed. Count information of the 8 cases was LogNormalized and integrated according to guidelines for fast integration with reciprocal PCA (rPCA) in Seurat
Integrated data were scaled using ScaleData function and regressing on “nCount_RNA”, “percent.mito”, “percent.ribo”, and “nFeature_RNA”. Scrublet v0.2.1 was used to remove doublets.
Unbiased clustering analysis (dim = 30, k.parameter = 10, res = 0.4)
Assembly: GRCh38
Supplementary files format and content: counts.txt, tab separated values, counts of every gene per nucleus
Supplementary files format and content: meta_data_counts.csv, comma separated values, meta data of every nucleus

source_name: SEZ

extract_protocol:
The SEZ tissues were lysed in a sucrose lysis buffer and the lysates were filtered through a 70 µm cell strainer. Then, nuclei were purified by ultracentrifugation through a dense sucrose buffer. After sucrose density centrifugation, ~ 40,000 DAPI positive events per sample were collected by FACS, and subjected to snRNAseq.
Single nucleus cDNA libraries were constructed according to the user guide of Chromium Single Cell 3’ Reagents Kit v3.1 (10x Genomics)

tag: tissue

value: SEZ

tag: age

tag: group

value: 1, middle-aged


title: rnc_GDSR_microaerob_1

description: Rhodobacter sphaeroides rnc mutant grown under microaerobic conditions, rep 1


title: C2C12, 96 hours after differentiation, biological replicate2


title: rnc_GDSR_aerob_3

description: Rhodobacter sphaeroides rnc mutant grown under aerobic conditions, rep 3


title: AY00898

description: Sample 5


title: SEZ, middle-aged, G, snRNA-seq

description: 10x Genomics


title: C2C12, 96 hours after differentiation, biological replicate1


title: rnc_GDSR_phototroph_1

description: Rhodobacter sphaeroides rnc mutant grown under phototrophic conditions, rep 1


title: rnc_GDSR_aerob_2

description: Rhodobacter sphaeroides rnc mutant grown under aerobic conditions, rep 2


title: AY00890

description: Sample 4


title: SEZ, middle-aged, E, snRNA-seq

description: 10x Genomics


title: rnc_GDSR_microaerob_3

description: Rhodobacter sphaeroides rnc mutant grown under microaerobic conditions, rep 3


title: rnc_GDSR_aerob_1

description: Rhodobacter sphaeroides rnc mutant grown under aerobic conditions, rep 1


title: SEZ, middle-aged, F, snRNA-seq

description: 10x Genomics


title: AY00883

description: Sample 3


title: C2C12, 144 hours after differentiation, biological replicate2


title: C2C12, 72 hours after differentiation, biological replicate3


title: SEZ, young, D, snRNA-seq

description: 10x Genomics

value: 0, youth


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 5, library 43_5_shallow, library 43_5_deep

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

country: United Kingdom

institute: University of Exeter

description: SPLiT-seq

data_processing:
Barcode processing and adapter trimming were made using SPLiT-seq toolbox (https://github.com/RebekkaWegmann/splitseq_toolbox), CutAdapt  v2.8 (https://github.com/marcelm/cutadapt), pairfq makepairs (https://github.com/sestaton/Pairfq) and Picard v2.21.1-SNAPSHOT (https://github.com/broadinstitute/picard)
Genome mapping was made with STAR-2.7.3a (https://github.com/alexdobin/STAR/releases/tag/2.7.3a)
Assembly: Genome assembly will be available on planmine (https://planmine.mpibpc.mpg.de/planmine/genome.do)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Whole-body

extract_protocol:
We used ACME dissociation to dissociate whole animals into fixed and permeable cell suspensions. Dissociated cells were proccessed using a SPLiT-seq protocol (we sorted singlets by FACS during SPLiT-seq, right before the cell lysis step).
We followed the SPLiT-seq library construction pipeline (Dynabeads cDNA purification, template switching, PCR amplification, size selection, tagmentation, indexed-PCR amplification and second size selection). Size selection was performed using Roche KAPA Pure Beads at 0.6X-0.8X ratios. Tagmentation was performed using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer´s instructions.

value: Whole-body

value: WT

value: RNAi


title: C2C12, 72 hours after differentiation, biological replicate2

value: wild type


title: AY00871

description: Sample 2


title: Capan2 cells, ChIPseq H3K27ac, Untreated, Rep1

value: PDAC Low-Grade

value: Wild type


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 4, library 43_4_shallow, library 43_4_deep

description: SPLiT-seq


title: AY00908

description: Sample 7


title: C2C12, 72 hours after differentiation, biological replicate1

value: 72 hours after differentiation


title: C2C12, 0 hours after differentiation, biological replicate3


title: SEZ, young, C, snRNA-seq

description: 10x Genomics


title: spleen tissue under bleeding

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

data_processing:
Raw reads were aligned to the pre-build mm10 reference genome using cellranger count v7.0.0 (10X Genomics) with default settings.
The molecule information files were combined using cell ranger aggr with --normalize=none --nosecondary options.
The R package Seurat v4.1.1 was used for downstream analysis.
Cells with UMI counts less than 500, fewer than 100 genes detected, or ≥ 7% of reads mapped to mitochondrial genes were removed.
Read counts were normalized using the Seurat SCTransform function with the option vst.flavor=“v2”.
Variation due to mitochondrial RNA ratio and cell cycle phase scores were regressed out.
The data were integrated based on the 3,000 most highly variable genes using the Seurat integration procedure.
Principal component analysis was performed using the Seurat RunPCA function.
Top 50 principal components were used for Uniform manifold approximation and projection and cell clustering.
Cell clustering was performed with the resolution “1.0”.
Differentially expressed genes between clusters or groups were estimated using the Seurat FindAllMarkers function with the option only.pos=TRUE.
Assembly: mm10
Supplementary files format and content: RDS file continaing a Seurat object with raw count data from three samples.
Supplementary files format and content: TSV file containig the result of differential gene expression (DGE) analysis

source_name: House mouse

growth_protocol: Spleen tissue were isolated from mice under steady state, 5 days post PHZ treatment and 5 days after the first serial bleeding.

extract_protocol:
Cells were washed, and processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions.
The library was prepared using 10xGenomics's Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and dual index kit following manufacturer's instructions.  Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.  Sequencing was done by DNBseq platform at BGI Genomics.

treatment_protocol: No treatment (WT/NT), PHZ and serial bleeding (BLD)

tag: cells

value: spleen cells bleeding


title: SEZ, young, B, snRNA-seq

description: 10x Genomics


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 3, library 43_3_shallow, library 43_3_deep

description: SPLiT-seq


title: AY00836

description: Sample 1

value: HGG


title: C2C12, 0 hours after differentiation, biological replicate2

value: 0 hours after differentiation


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 2, library 43_2_shallow, library 43_2_deep

description: SPLiT-seq


title: SEZ, young, A, snRNA-seq

description: 10x Genomics


title: bone marrow cells no treatment (BW_NT)

data_processing:
Raw reads were aligned to the pre-build mm10 reference genome using cellranger count v7.0.0 (10X Genomics) with default settings.
The molecule information files were combined using cell ranger aggr with --normalize=none --nosecondary options.
Cells with UMI counts less than 500, fewer than 100 genes detected, or ≥ 7% of reads mapped to mitochondrial genes were removed.
Read counts were normalized using the Seurat SCTransform function with the option vst.flavor=“v2”.
Variation due to mitochondrial RNA ratio and cell cycle phase scores were regressed out.
The data were integrated with three spleen samples (WT, PHZ and BLD) based on the 3,000 most highly variable genes using the Seurat integration procedure.
Principal component analysis was performed using the Seurat RunPCA function. Top 50 principal components were used for Uniform manifold approximation and projection and cell clustering.
Cell clustering was performed with the resolution “1.0”.
Differentially expressed genes between clusters or groups were estimated using the Seurat FindAllMarkers function with the option only.pos=TRUE.
Assembly: mm10
Supplementary files format and content: RDS file continaing a Seurat object with raw count data from four samples (WT, PHZ, BLD and BW_WT).
Supplementary files format and content: TSV file containig the result of differential gene expression (DGE) alaysis using the BM_WT sample only.

source_name: spleen cells no treatment

growth_protocol: Bone marrow cells were isolated from mice under steady state.

extract_protocol:
Cells were washed, and processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions.
Single cell RNA-Seq (3'GEM); The library was prepared using 10xGenomics's Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and dual index kit following manufacturer's instructions.  Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.  Sequencing was done by DNBseq platform at BGI Genomics.

treatment_protocol: No treatment (NT).

value: Bone marrow cells

tag: strain


title: Schmidtea mediterranea, whole-body, scRNA-seq, batch 1, library 43_1_shallow, library 43_1_deep

description: SPLiT-seq


title: C2C12, 0 hours after differentiation, biological replicate1


title: case #1 of PRCC

status: Public on Feb 18 2024

city: San Sebastian

first: Stéphane

last: Nemours

state: Guipúzcoa

address: Paseo Dr. Begiristain, s/n

country: Spain

institute: Biogipuzcoa

hyb_protocol: none provided

scan_protocol: GeneChips were scanned using theAffymetrix gene chip scanner 3000, GCS3000 DX system .

data_processing: The raw intensity data (i.e., cel files) were imported and analysed within Transcriptome Analysis Console (TAC) software version 4.0.2 (Affymetrix, USA)

label: biotin

source_name: PRCC case

label_protocol: We used 200ng of DNAse treated RNA for Clariom D human microarrays to measure gene expression. RNA was labelled and hybridised to microarrays in accordance with the manufacturer’s instructions (Affymetrix, USA).

extract_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) biopsy material using the Recover All kit from Ambion (LifeTechnologies, UK) according to the manufacturer's instructions.

value: PRCC


title: case #2 of PRCC


title: case #7 of PRCC


title: case #9 of PRNRP

source_name: PRNRP case

value: PRNRP


title: case #6 of PRCC


title: case #4 of PRCC


title: spleen tissue no treatment (NT)

value: spleen cells no treatment


title: case #6 of PRNRP


title: case #5 of PRNRP


title: case #3 of PRCC


title: spleen tissue under PHZ

value: spleen cells PHZ


title: case #7 of PRNRP


title: case #5 of PRCC


title: case #10 of PRNRP


title: case #3 of PRNRP


title: case #2 of PRNRP


title: case #4 of PRNRP


title: Monocyte/macrophage CGRP rep1

city: Clayton

first: Mikaël

last: Martino

state: VICTORIA

address: 15 Innovation Walk, Clayton, VIC

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
Processed_Mono_Macro_data.csv
Mono_Like_CGRP_1

data_processing:
Fastq files were processed using the nfCore/RNAseq (v3.2) pipeline using the umi function (Patel, H., Ewels, P. & Peltzer, 2013, A. nf-core/rnaseq: nf-core/rnaseq v3.2 - Copper Flamingo, Zenodo)
Reads were aligned to the Mus musculus GRCm38 reference using STAR aligner (Dobin, A., et al., 2013, Bioinformatics)
Reads were quantified using featureCounts (Liao, Y., et al., 2014, Bioinformatics) producing the raw genes count matrix and various quality control metrics.
Raw counts were then analysed with Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol)
Assembly: GRCm38
Supplementary files format and content: csv file where rows represent genes and each column represents different information, including gene name, gene ID and raw gene counts corresponding to the individual samples.

source_name: bone marrow-derived

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
RNA samples (20 ng) with RIN value ≥ 7 were used for library preparation. First strand synthesis was performed using a dT primer which also adds the Illumina P7 (5ʹ CAA GCA GAA GAC GGC ATA CGA GAT 3ʹ), 8 bp i7 index for each sample and a 10 bp unique molecular identifier (UMI). The modified reverse transcriptase reaction also adds a template switching sequence at the 5’ end of the RNA during the generation of indexed cDNA. These first stand indexed cDNA were pooled and amplified using primers to P7 and the template switch sequence. The Illumina P5 was added by tagmentation by Nextera transposase during amplification. The standard Illumina R1 primer was used (main cDNA read), followed by standard i7 primer for index/UMI. The R2 primer was present but not used as it will read into poly-A tail.

treatment_protocol: Freshly isolated neutrophils were treated with CGRP (1 nM) in RPMI with 10% FBS and 100 units/ml penicillin/streptomycin for 4 hours at 37°C with 5% CO2. Freshly isolated monocytes were cultured in DMEM/F12 with 10% FBS, 100 units/ml penicillin/streptomycin, and M-CSF (10 ng/ml) for 3 days. The cell culture medium was replaced with medium containing CGRP (1 nM) for 4 hours at 37°C with 5% CO2.

value: bone marrow-derived

value: monocytes/macrophages

value: CGRP (1 nM) treatment


title: Monocyte/macrophage PBS rep3

description:
Processed_Mono_Macro_data.csv
Mono_Like_PBS_3

value: PBS (Saline control)


title: Monocyte/macrophage CGRP rep3

description:
Processed_Mono_Macro_data.csv
Mono_Like_CGRP_3


title: Monocyte/macrophage CGRP rep2

description:
Processed_Mono_Macro_data.csv
Mono_Like_CGRP_2


title: Monocyte/macrophage PBS rep2

description:
Processed_Mono_Macro_data.csv
Mono_Like_PBS_2


title: Neutrophils CGRP rep3

description:
Processed_Neutrophil_data.csv
Neu_CGRP3

value: neutrophils


title: Neutrophils CGRP rep1

description:
Processed_Neutrophil_data.csv
Neu_CGRP1


title: Neutrophils CGRP rep2

description:
Processed_Neutrophil_data.csv
Neu_CGRP2


title: case #8 of PRNRP


title: Neutrophils PBS rep3

description:
Processed_Neutrophil_data.csv
Neu_PBS3


title: Neutrophils PBS rep2

description:
Processed_Neutrophil_data.csv
Neu_PBS2


title: 026_tumor

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th Ave NE

institute: The Hormel Institute

data_processing:
Quality check for sequencing data and probes, as well as data exploration were done  by using the GeoMx DSP analysis suite
Supplementary files format and content: Probe counts in the ROI
Library strategy: GeoMx NGS

source_name: Liver metastasis tumor

extract_protocol:
Two months old Glut1F/F mice (control mice) and Glut1F/FPRβ-CreERT2 mice (conditional Glut1 knockout mice) were received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-CD45 for immune cells, and SYTO 13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+ CD45-) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin- CD45-) within a same ROI were collected for transcriptomic profiling as well. Segments 17-20 were ROIs from Glut1F/FPRβ-CreERT2 mice and 21-26 were from Glut1 F/F mice. 20 sequencing data were generated for the CAFs due to dual-indexing primers-based sequencing, which was done on Illumina NextSeq 2000.
immunofluorescence (IF) staining was performed using commercially available antibodies against Desmin (Ab32362 abcam, 1:400 dilution) and CD45 (NovusBio, NBP1-44763).  Slides were blocked with Buffer W probes (NanoString Technologies, Cat#121300313) at room temperature for 2 hours.  Anti-desmin unconjugated primary antibody was incubated overnight at 4°C.  Slides were washed three times in 2XSSC and then incubated for 2 hours with anti-rabbit secondary antibody conjugated to Alexa Fluor 647 (Thermofisher, # A-21244) (1:500 dilution), CD45 directly conjugated antibody (AF532) and SYTO 13 fluorescent nucleic acid stain (ThermoFisher, Cat# S7575) were followed
Prepared tissues were flooded with whole transcriptome RNA probes (NanoString Technologies, Cat#121401102) attached to oligonucleotide barcodes via photocleavable linkers.  Slides were covered with HybriSlip hybridization covers (Grace Bio-Labs, Cat#714022) and hybridized overnight at 37°C in a hybridization oven (Boekel Scientific RapidFISH Slide Hybridizer, Cat#240200).  Following hybridization, unbound probes were washed away using a solution of equal parts 4XSSC and deionized formamide (ThermoFisher, Cat#AM9342)
Slides were loaded and scanned in the Nanostring GeoMx DSP instrument.  Exposure times for each channel were optimized and set to 100 ms (FITC), 600 ms (Texas Red) and 250 ms (Cy5).  Circular ROIs ranging form approximately 400 – 660 microns were drawn on the resulting images utilizing Desmin IF staining for guidance.  ROI masks were created using the GeoMx DSP Control Center software by utilizing the fluorescence intensity of the immunofluorescence staining.  The thresholding of each segment was adjusted for each ROI to accommodate for IF staining heterogeneity. Segments were selected for CAFs (desmin positive and CD45 negative regions), and tumor regions (desmin and CD45 negative regions; reminder).  Selected segments were illuminated by UV laser in the GeoMx instrument and photocleaved barcodes were collected and deposited into a 96-well microplate by the instruments onboard microfluidics system.  Collection plates were sealed to prevent contamination and stored at -80°C prior to library preparation.

tag: segment (name/ label)

value: Remainder

value: MC38 adjacent to Fibroblast

value: control


title: 023_tumor


title: Neutrophils PBS rep1

description:
Processed_Neutrophil_data.csv
Neu_PBS1


title: 024_tumor


title: 025_tumor


title: 021_tumor


title: 019_tumor


title: 020_tumor


title: 022_tumor


title: 026_CAF

value: Desmin

value: Liver metastasis tumor

value: Fibroblast


title: COX2452A6,Hhepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,4

city: London

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

data_processing:
sequencing quality control done with FLEXBAR software
sequencing reads mapped to mm10 genome and the GENCODE reference transcriptome version M22 with STAR software
Raw gene counts were retrieved using QoRTs software
Normalised read counts were retrieved using DeSeq2

source_name: colon lamina propria

growth_protocol: Helicobacter hepaticus (NCl-Frederick isolate 1A, strain 51449) was grown under anaerobic gas conditions 10% CO2, 10% H2/N2 (BOC) on blood agar plates containing 7% laked horse blood (Thermo Scientific) and the campylobacter selective supplement (Skirrow) antibiotics trimethoprim, vancomycin and polymyxin B (all from Oxoid). Cultures were then transferred to and expanded, again under the anaerobic gas conditions above, for 3-4 days to OD 0.6 in tryptone soya broth (Oxoid) supplemented with 10% FCS (Gibco) and the antibiotics above.

extract_protocol:
On Day 14 following infection with Helicobacter hepaticus, colon lamina propria leukocytes were isolated from individual  infected and uninfected control mice and CD4+ T cells were sorted. RNA was extracted using the QIAShredder and RNeasy Mini Kit with on-column DNase digestion, according to the manufacturer’s instructions (Qiagen).
RNA-seq libraries were then made with total RNA using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina and unique multiplexing indexes, according to the manufacturer’s instruction (New England Biolabs).

treatment_protocol: Mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: colon lamina propria

value: sorted CD4+ T cells

value: Prdm1 fl/fl Maf fl/fl CD4-Cre

value: Hhepaticus


title: 024_CAF


title: 025_CAF


title: COX2452A8,Hhepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,6


title: case #1 of PRNRP

value: PRNRP


title: 018_tumor


title: 017_tumor


title: Monocyte/macrophage PBS rep1

description:
Processed_Mono_Macro_data.csv
Mono_Like_PBS_1


title: COX2452A5,Hhepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,3


title: 022_CAF


title: COX2452A4,Hhepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,2


title: 021_CAF


title: COX2452A3,Hhepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,1


title: COX2452A9,Hhepaticus_Maf fl/fl CD4-Cre,6

value: Maf fl/fl CD4-Cre


title: 020_CAF


title: COX2452A24,Hhepaticus_Maf fl/fl CD4-Cre,5


title: 019_CAF


title: COX2452A23,Hhepaticus_Maf fl/fl CD4-Cre,4


title: COX2452A11,Hhepaticus_Maf fl/fl CD4-Cre,2


title: 017_CAF


title: COX2452A7,Hhepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,5


title: COX2452A10,Hhepaticus_Maf fl/fl CD4-Cre,1


title: COX2452A22,Hhepaticus_Maf fl/fl CD4-Cre,3


title: COX2452A26,Hhepaticus_Prdm1 fl/fl CD4-Cre,4

value: Prdm1 fl/fl CD4-Cre


title: 018_CAF


title: human dental pulp cells, alpha minimum essential medium, 5 days, rep2

city: Seoul

first: Yong Kwon

last: Chae

address: Kyungheedaero 26

country: South Korea

institute: Kyung Hee University Dental Hospital

data_processing:
high-quantity sequencing was carried out on single-read 75 bp fragments via the NextSeq 500 platform (Illumina Inc.).
Bowtie2 was used for aligning the QuantSeq 3′ mRNA‐Seq reads (Langmead & Salzberg 2012).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: dental pulp

extract_protocol:
RNA was isolated with Trizol reagent (Invitrogen).
The QuantSeq 30 mRNA-Seq Library Prep Kit (Lexogen Inc.) was used in the preparation of RNA library following manufacturer's protocol.

value: dental pulp

value: human dental pulp cells

value: α-MEM


title: COX2452A12,Hhepaticus_Prdm1 fl/fl CD4-Cre,1


title: human dental pulp cells, alpha minimum essential medium, 5 days, rep1


title: COX2452A25,Hhepaticus_Prdm1 fl/fl CD4-Cre,3


title: human dental pulp cells, G-Rb1 treated, 5 days, rep1


title: human dental pulp cells, untreated, 0 day

value: no treatment


title: COX2452A2,Hhepaticus_Prdm1 fl/fl Maf fl/fl,4

value: Prdm1 fl/fl Maf fl/fl


title: A13A_P_Ctrl, Rep3 (ATAC-seq)

city: Oxford

first: Siim

last: Pauklin

state: United Kingdom

address: Botnar Research Centre,

institute: University of Oxford

data_processing:
Sequencing  reads  from  the  ATAC seq experiment  were  aligned  to  the  human  genome  (hg38)  using bowtie with reporting mode,” –best –strata –v2”.Deeptools was used to generate covergae track(bigwig). Coverage track was visualized by using UCSC genome browser. Peak calling was performed by using macs2 peak caller with default parameters for ChIP seq, and with parameter “--nomodel --shift -100 --extsize 200” for ATAC seq. Peaks annotated with nearest gene information by using BEDTools. Peak distribution over different genomic features were summarized by using Bioconductor package ChiPpeakAnno. Motif enrichment analysis within peak regions was performed using HOMER. All plots were generated using R package 3.6.
Assembly: hg38
Supplementary files format and content: peaks.bed and TSS_Information.tsv files

source_name: CSC

growth_protocol: For standard cell cultures, cells were grown at 37°C humidiﬁed incubator containing 5% CO2 in Dulbeccos modified Eagles medium (DMEM), high glucose, GlutaMAX™ Supplement, pyruvate (Thermo Fisher Scientific, Inc.), 100 U/ml penicillin, 100 mg/ml streptomycin (Thermo Fisher Scientific, Inc.), MEM Non-Essential Amino Acids Solution 1X (Life Technologies; Thermo Fisher Scientific), MEM Vitamin Solution 1X (Life Technologies; Thermo Fisher Scientific) and 10% inactivatedfetal calf serum (FCS; Life Technologies). For 3D cultures, cells we grown in ultra-low attachment plates (Thermo Fisher Scientific, Inc.) in Dulbecco’s Modified Eagle Medium/F12 (Sigma-Aldrich) supplemented with 2.5mM L-Glutamine (Thermo Fisher Scientific, Inc.), 1% B27 supplement (Life Technologies), 100 U/ml penicillin, 100 mg/ml streptomycin (Thermo Fisher Scientific, Inc.), 20ng/ml basic thermostable fibroblast growth factor (FGF-Basic TS, Proteintech) (5,000 cells/ml).

extract_protocol:
Cells were washed once with PBS, collected in Cell Dissociation Buffer (Gibco 13150-016) or TrypLE and centrifuged at 300g for 3 min. The cell pellets were then resuspended in 2 ml of 4°C PBS and counted by haemocytometer for using 100,000 cells in the subsequent step. Cells were centrifuged at 300g for 3 min, the supernatant aspirated, the cell pellet resuspended in 150 ul of Isotonic Lysis Buffer (10 mM Tris-HCl pH 7.5, 3 mM CaCl, 2 mM MgCl2, 0.32 M Sucrose and Protease Inhibitors, Roche), and incubated for 12 min on ice. Triton X-100 from a 10% stock was then added at a final concentration of 0.5%, the samples were vortexed briefly and incubated on ice for 6 min. The samples were centrifuged for 5 min at 400g at 4°C, and the cytoplasmic fraction removed from the nuclear pellet. The samples were resuspended gently in 625uL of PBS and transferred to a fresh 1.5 ml eppendorf tube. The nuclei were centrifuged at 1500g for 3 min at 4°C and the supernatant aspirated thoroughly from the nuclear pellet. This step was immediately followed by tagmentation (Nextera DNA Sample Preparation Kit for 24 Samples, FC-121-1030) by resuspending each sample in 100 µL Nextera mastermix (52.5 µl TD buffer, 42.5 µl of water and 5 µl of TDE1 per reaction).
PCR reaction (for all samples including control sample) was performed with the following constituents: 10 µl template from tagmentation, 2.5 µl I7 primer (Nextera® Index Kit with 24 Indices for 96 Samples, FC-121-1011), 2.5 µl I5 primer, 10 uL Nudease Free H2O 25µl NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M054 and 10 uL Nuclease Free H2O. The PCR settings were as follows: at 72 °C for 5 miutes, initial denaturation at 98 °C for 30 seconds, then 12 cycles of 98 °C for 10 seconds, primer annealing at 63 °C for 30 seconds and elongation at 72 °C for 1 minute, and holding at 4 °C. After completing the PCR, the sample were stored at -20 °C.
The PCR primers were removed with 1 x 0.9:1 SPRI beads (Beckman Coulter, Cat no. A63880) according to manufacturer’s protocol and samples eluted in 20 µl. 2 µl of the samples were run on Agilent HS Bioanalyzer HS for confirming the size selection of the ATAC libraries. ATAC-sequencing was performed by Illumina HiSeq 2000 sequencing with 75 bp PE for obtaining more than 40 million mapped reads per library.

value: Pancreatic cancer

value: PDAC

value: WT

value: Suspension


title: human dental pulp cells, G-Rb1 treated, 5 days, rep2


title: COX2452A17,Hhepaticus_Prdm1 fl/fl Maf fl/fl,2


title: A13A_P_Ctrl, Rep2 (ATAC-seq)


title: COX2452A18,Hhepaticus_Prdm1 fl/fl Maf fl/fl,3


title: COX2452A1,Hhepaticus_Prdm1 fl/fl Maf fl/fl,1


title: 023_CAF

value: Desmin

value: Liver metastasis tumor

value: Fibroblast

value: control


title: PM cells,Igf2bp3-KO,VSV-rep1

city: Suzhou

first: Siying

last: Liu

state: Jiangsu

address: 111 Ren’ai Road

institute: Xi'an Jiaotong-Liverpool University

data_processing:
Raw data from the pair-end sequencing reads were firstly processed using the fastp software to trim the adapter sequences and discard reads which are short or in poor quality
The refined reads were mapped to the reference genome (GRCm38.p6) with hisat2
The fold changes and p-values of genes between the groups were calculated using DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: xlsx
Supplementary files format and content: FPKM of all genes on GRCm38.p6

source_name: PM

extract_protocol:
Total RNAs from the cells were then extracted using the Trizol reagent, following manufacturer' s instructions.
The cDNA libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (No. NR605, Vazyme)

treatment_protocol: WT/Igf2bp3-KO RAW264.7 cells and PMs were infected VSV-GFP (MOI=1) for 8 hours.

value: PM

value: Igf2bp3 knockout

value: VSV infection


title: PM cells,Igf2bp3-KO,VSV-rep3


title: A13A_P_Ctrl, Rep1 (ATAC-seq)


title: PM cells,WT,VSV-rep3

value: wildtype


title: human dental pulp cells, alpha minimum essential medium, 5 days, rep3

value: dental pulp


title: COX2452A21,Uninfected_Prdm1 fl/fl Maf fl/fl CD4-Cre,3

value: colon lamina propria

value: sorted CD4+ T cells

value: Prdm1 fl/fl Maf fl/fl CD4-Cre

value: Uninfected


title: PM cells,WT,VSV-rep2


title: PM cells,Igf2bp3-KO,VSV-rep2


title: COX2452A20,Uninfected_Prdm1 fl/fl Maf fl/fl CD4-Cre,2


title: A13A_Adh_Ctrl, Rep3 (ATAC-seq)

source_name: non-CSC

value: Pancreatic cancer

value: Adherent culture


title: RAW264.7 cells,Igf2bp3-KO,VSV-rep2


title: A13A_Adh_Ctrl, Rep2 (ATAC-seq)

value: PDAC

value: WT


title: PM cells,WT,VSV-rep1


title: human dental pulp cells, G-Rb1 treated, 5 days, rep3

value: human dental pulp cells


title: COX2452A13,Hhepaticus_Prdm1 fl/fl CD4-Cre,2

value: Prdm1 fl/fl CD4-Cre

value: Hhepaticus


title: COX2452A19,Uninfected_Prdm1 fl/fl Maf fl/fl CD4-Cre,1


title: A13A_Adh_Ctrl, Rep1 (ATAC-seq)


title: RAW264.7 cells,Igf2bp3-KO,VSV-rep1


title: COX2452A16,Uninfected_Prdm1 fl/fl Maf fl/fl,3

value: Prdm1 fl/fl Maf fl/fl


title: A13A_P_Ctrl, Rep3 (RNA-seq)

description: A13A_RNAseq_Count table

data_processing:
Sequencing reads  from  the  RNA-seq  experiment  were  aligned  to  the  human  genome  (hg38)  using HISAT2 with the default parameters. FeatureCounts was used to assign mapped reads to genes with annotation gtf file Ensembl94. Differential gene expression analysis was performed using DESeq2 with IHW method for p value adjustment, apeglm method for effect size shrinkage, FDR-adjusted p value < 0.05 and log2 fold change > 0. Functional analysis of differential expressed genes was performed using Metacore. All plots were generated using R package 3.6.
Assembly: hg38
Supplementary files format and content: tab-delimited text file representing counts for all samples

extract_protocol:
RNA was extracted using Direct-zol (TM) RNA extraction kit according to manufacturer protocol (Cambridge Bioscience, R2052). The quality of the RNA samples was verified using an RNA screen tape on a Tape-Station (Agilent). The RIN values for all samples were >7.5.
RNA-Seq libraries were created using the NEBNext Ultra RNA library prep kit using TruSeq indexes, following the manufacturer’s recommendations. In summary, 500 ng of total RNA was used to isolate mRNA poly(A) by two rounds of purification using oligo dT magnetic beads followed by fragmentation and cDNA synthesis by random primers and reverse transcriptase. Bar-coded adapters were ligated to the cDNA fragments and a PCR reaction was performed to produce the sequencing libraries. To verify the library concentration and the library fragments length was used Agilent 2200 Tape-Station System. Adapter-ligated cDNA fragment libraries were sequenced on a NextSeq 500 platform (Illumina) using a paired-end run (2 × 41 bp).

value: Suspension


title: RAW264.7 cells,ctrl,VSV-rep2


title: RAW264.7 cells,ctrl,VSV-rep3


title: RAW264.7 cells,ctrl,VSV-rep1


title: COX2452A15,Uninfected_Prdm1 fl/fl Maf fl/fl,2


title: Ai9_pos_2

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: growth plate

extract_protocol:
Total RNA extraction using Trizol reagent
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: growth plate

value: primary cells

value: chondrongenic cells

value: Tdtomato+

tag: strain background


title: Ai9_pos_3


title: Ai9_pos_1


title: COX2452A14,Uninfected_Prdm1 fl/fl Maf fl/fl,1

value: colon lamina propria


title: A13A_P_Ctrl, Rep1 (RNA-seq)

description: A13A_RNAseq_Count table


title: COX2453A9,H. hepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,6

data_processing:
Sequencing quality control done with Skewer 0.2.2
Sequencing reads mapped to mm10 with BWA-MEM
Duplicates were removed using Picard
Alignment QC, discarded alignments with a mapQ below 30 using SAMtools 1.3.1
Discarded alignemnts done to mitochondrial DNA, shifted Reads to represent the Tn5 insertion, and remove fragments spanning nucleosomes (size >99 bp) using awk and BEDTools 2.4.2. Fragments spanning nucleosomes were not removed for the one untreated sample
MACS2 2.1.1 (parameters --keep-dup all, --nomodel, --shift -100, --extsize 200) was used to call peaks (q-value < 0.01)
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Assembly: mm10
Supplementary files format and content: Bigwig files are provided fro ATAC-seq data normalised to RPKMs (fragments spanning nucleosomes excluded), for peaks called bed files are provided

extract_protocol:
On Day 14 following infection with Helicobacter hepaticus, colon lamina propria leukocytes were isolated from individual  infected and uninfected control mice and CD4+ T cells were sorted. 50,000 cells were lysed with cold ATAC-seq lysis buffer containing 10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Nonidet™ P40 substitute (all Sigma) and the nuclei incubated for 2 hours at 37°C with 50μl of TDE1/TD transposase reaction mix (Illumina).
Tagmented DNA was purified using the MinElute kit (Qiagen) and amplified under standard ATAC PCR conditions: 72°C for 5 min; 98°C for 30s and thermocycling at 98°C for 10s, 63 °C for 30s and 72°C for 1 min for 12 cycles. Following amplification, ATAC-seq libraries were cleaned up using 90μl of AMPure XP beads (Beckman Coulter) and two 80% Ethanol washes whilst being placed on a magnetic plate stand, before being eluted in 1mM (0.1x) Tris-EDTA buffer, pH8 (Sigma) diluted with DEPC-treated water (Ambion).

value: sorted CD4+ T cells

value: H. hepaticus


title: A13A_Adh_Ctrl, Rep3 (RNA-seq)

description: A13A_RNAseq_Count table


title: RAW264.7 cells,Igf2bp3-KO,VSV-rep3

value: Igf2bp3 knockout

value: VSV infection


title: COX2453A8,H. hepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,5

value: Prdm1 fl/fl Maf fl/fl CD4-Cre


title: A13A_Adh_Ctrl, Rep2 (RNA-seq)

description: A13A_RNAseq_Count table

value: Pancreatic cancer

value: PDAC

value: Adherent culture


title: liver, WPF2

city: Tianjin

first: Jiaqi

last: Li

state: None Selected

address: No.94 Weijin Road, Nankai District

institute: Nankai university

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: Species: mus_musculus Origin: ensembl Version: GRCm39.107
Supplementary files format and content: all.fpkm_anno.txt file includes counts and FPKM for each Sample

source_name: WT mice fed with HFrD diet during pregnancy

extract_protocol:
RNA was harvested using Trizol Reagent (MAGEN Inc., China).1 μg total RNA was used for library preparation.
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: liver

value: WT

value: HFrD diet during pregnancy


title: A13A_Adh_Ctrl, Rep1 (RNA-seq)

description: A13A_RNAseq_Count table


title: liver, WPF4


title: liver, KPF3

source_name: hChrebp-KO mice fed with HFrD diet during pregnancy

value: hChrebp-KO


title: liver, WPF3


title: COX2453A4,H. hepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,3


title: 5_shNT_CD133p

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description: stable control sh (shNT) infected cells sorted according to CD133 marker. This population in positive to CD133 expression

data_processing:
Analysis was performed with the UTAP pipeline (Kohen et. al., BMC Bioinformatics . 2019).
Data analysis was performed by using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Raw reads were trimmed using cutadapt with the parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A–times 2 -u 3 -u −3 -q 20 -m 25). Reads were mapped to the genome (mm10, Gencode annotation version 10.0) using STAR (v2.4.2a) with the parameters –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No. The pipeline quantifies the 3′ of Gencode annotated genes (The 3′ region contains 1,000 bases upstream of the 3′ end and 100 bases downstream). UMI counting was done after marking duplicates (in-house script) using HTSeq-count in union mode. Only reads with unique mapping were considered for further analysis, and genes having minimum 5 reads in at least one sample were considered. Gene expression levels were calculated and normalized using DESeq2
Assembly: hg38
Supplementary files format and content: excel, count matrix,

source_name: Endometrial Cancer, HEC-1A, CD133 sorted

extract_protocol:
15,000 CD133+ or CD133- conteol or EIF4G2KD cells were FACS sorted into 40 μL of lysis binding buffer and mRNA was isolated using Dynabeads mRNA DIRECT Purification Kit (Thermo-Fisher scientific; cat# 61012) according to manufacturer’s protocol. In brief, a bulk variation of MARSseq6 was used to prepare libraries for RNA-seq. RNA was reversed transcribed with MARSseq barcoded RT primer in a 10 mL volume with the Affinity Script kit (Agilent). Reverse transcription was analyzed by qRT-PCR and samples with a similar CT were pooled (up to eight samples per pool). Each pool was treated with Exonuclease I (NEB) for 30 min at 37°C and subsequently cleaned by 1.2 x volumes of SPRI beads (Beckman Coulter). Subsequently, the cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20mL reaction, incubating for 2 h at 16°C. The product was purified with 1.4 x volumes of SPRI beads, eluted in 8 mL and in vitro transcribed (with the beads) at 37°C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37°C and the amplified RNA (aRNA) purified with 1.2 volumes of SPRI beads. The aRNA was fragmented by incubating 3 min at 70°C in Zn2+ RNA fragmentation reagents (Ambion) and purified with 2 x volumes of SPRI beads. The aRNA was ligated to the MARS-seq ligation adaptor with T4 RNA Ligase I (NEB). The reaction was incubated at 22°C for 2 h. After 1.5 x SPRI cleanup, the ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent) and a primer complementary to the ligated adaptor. The reaction was incubated for 2 min at 42°C, 45 min at 50°C, and 5 min at 85°C. The cDNA was purified with 1.5 x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5mM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kappa Biosystems). The amplified pooled library was purified with 0.7 x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument. RNaseq libraries were sequenced using the Illumina NextSeq 2000.
MARS-seq 2.0. DOI: 10.1038/s41596-019-0164-4

value: HEC-1A endomertial cell line was infected with shGFP (shNT) as control. The control cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations.


title: liver, KPF2


title: COX2453A14,H. hepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,2


title: A13A_P_Ctrl, Rep2 (RNA-seq)

description: A13A_RNAseq_Count table

value: Suspension


title: 5_shNT_CD133-

description: stable control sh (shNT) infected cells sorted according to CD133 marker. This population in negative to CD133 expression


title: PC1

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: Species: mus_musculus Origin: ensembl Version: GRCm39.107
Supplementary files format and content: all.fpkm_anno.xls file includes counts and FPKM for each Sample

source_name: liver

value: pregnancy with normal diet


title: COX2453A12,H. hepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,1


title: PC2


title: 5_shDAP5_CD133p

description: stable EIF4G2 KD (shDAP5) cells sorted according to CD133 marker. This population is positive to CD133 expression

value: HEC-1A endomertial cell line was KD with shRNA for EIF4G2 (DAP5) . The  cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations.


title: Ai9_neg_3

value: growth plate

value: primary cells

value: chondrongenic cells

value: Tdtomato-


title: PF2

value: pregnancy with HFrD diet


title: Ai9_neg_2


title: COX2453A35,H. hepaticus_Maf fl/fl CD4-Cre,6

value: colon lamina propria

value: sorted CD4+ T cells

value: Maf fl/fl CD4-Cre

value: H. hepaticus


title: Ai9_neg_1


title: 5_shDAP5_CD133-

description: stable EIF4G2 KD (shDAP5) cells sorted according to CD133 marker. This population is negative to CD133 expression


title: COX2453A34,H. hepaticus_Maf fl/fl CD4-Cre,5


title: PF1

value: liver


title: COX2453A5,H. hepaticus_Prdm1 fl/fl Maf fl/fl CD4-Cre,4

value: Prdm1 fl/fl Maf fl/fl CD4-Cre


title: 4_shNT_CD133p


title: IS-caput, Busulfan, rep3

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
NovaSeq6000 (Illumina) using 101 bp single-ended mode
sequence reads were mapped onto mouse reference genome (mm10) using TopHat ver. 2.1.1
Fragments Per Kilobase of exon per Million mapped reads (FPKM) values for each gene were calculated using Cufflinks ver. 2.2.1
Assembly: mm10
Supplementary files format and content: A Microsoft Excel file including FPKM values for each Sample

source_name: IS-caput epididymis

extract_protocol:
RNA was harvested using RNeasy (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

value: Wild-type

value: IS-caput epididymis

value: intraperitoneal injection of Busulfan


title: IS-caput, Busulfan, rep1


title: liver, KPF1

value: hChrebp-KO

value: HFrD diet during pregnancy


title: 4_shNT_CD133-

value: HEC-1A endomertial cell line was infected with shGFP (shNT) as control. The control cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations.


title: COX2453A20,H. hepaticus_Maf fl/fl CD4-Cre,3


title: IS-caput, Busulfan, rep2


title: IS-caput, DMSO, rep2

value: intraperitoneal injection of DMSO


title: PC3

value: WT

value: pregnancy with normal diet


title: IS-caput, DMSO, rep3


title: IS-caput, DMSO, rep1


title: COX2453A18,H. hepaticus_Maf fl/fl CD4-Cre,2


title: PF3


title: COX2453A38,H. hepaticus_Prdm1 fl/fl CD4-Cre,4

value: Prdm1 fl/fl CD4-Cre


title: 4_shDAP5_CD133-

value: HEC-1A endomertial cell line was KD with shRNA for EIF4G2 (DAP5) . The  cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations.


title: 3_shNT_CD133p

description:
stable control sh (shNT) infected cells sorted according to CD133 marker. This population in positive to CD133 expression
This sample did not pass QC test and therefore no processed data are provided for this sample as it was excluded from the analysis.


title: COX2453A15,H. hepaticus_Maf fl/fl CD4-Cre,1

value: colon lamina propria


title: 3_shNT_CD133-


title: 3_shDAP5_CD133p


title: 2_shNT_CD133p


title: COX2453A37,H. hepaticus_Prdm1 fl/fl CD4-Cre,3

value: sorted CD4+ T cells


title: 3_shDAP5_CD133-


title: COX2453A21,H. hepaticus_Prdm1 fl/fl CD4-Cre,1


title: COX2453A22,H. hepaticus_Prdm1 fl/fl CD4-Cre,2


title: COX2453A27,H. hepaticus_Prdm1 fl/fl Maf fl/fl,4

value: Prdm1 fl/fl Maf fl/fl


title: Maf fl/fl  Cd4Cre_Infected.3

description:
10x Genomics v3.1
ALV5070A16

data_processing:
Fastq files were aligned to the mm10 transcriptome, and count matrices were generated, filtering for GEM cell barcodes (excluding GEMs with free floating mRNA from lysed or dead cells) using Cell Ranger version 6.1.2.
Count matrices were imported to R and processed using the Seurat library (version 4.0) following the standard pipeline (Hao et al. 2021).
Low quality cells were removed, with cells kept for further analysis if they met the following criteria: the mitochondrial content was within 3 standard deviations from the median, more than 500 genes were detected and more than 1,000 RNA molecules were detected
DoubletFinder was used to identify doublets, assuming a theoretical doublet rate of 7.5%
All samples were integrated using the CCA method, implemented by Seurat’s functions FindIntegrationAnchors() and IntegrateData(), using the top 10000 variable features and the first 50 principal components
Assembly: A final manually curated annotation was assigned to clusters based on scMCA and clustifyr results, this resulted in the annotation of 17 distinct cell clusters
Supplementary files format and content: tab delimted txt file per sample showing features (rows) and cells (columns).

extract_protocol:
On Day 14 following infection with Helicobacter hepaticus, colon lamina propria leukocytes were isolated from individual infected and uninfected control mice and scRNA-seq was perfomed on total colon LPL. 10,000 cells per replicate were loaded into the 10x Chromium chips
scRNA-seq libraries were prepre according to the manufacturer's instructions- Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index)

value: colon LPL

value: Maf fl/fl  Cd4Cre

value: Infected


title: 2_shNT_CD133-


title: Prdm1fl/fl Cd4Cre_Infected.3

description:
10x Genomics v3.1
ALV5070A15

value: Prdm1fl/fl Cd4Cre


title: 4_shDAP5_CD133p


title: COX2453A32,H. hepaticus_Maf fl/fl CD4-Cre,4

value: Maf fl/fl CD4-Cre

value: H. hepaticus


title: COX2453A26,H. hepaticus_Prdm1 fl/fl Maf fl/fl,3


title: 2_shDAP5_CD133p


title: 2_shDAP5_CD133-


title: Maf fl/fl  Cd4Cre_Infected.2

description:
10x Genomics v3.1
ALV5070A14


title: Prdm1fl/fl Cd4Cre_Infected.2

description:
10x Genomics v3.1
ALV5070A13


title: COX2453A2,H. hepaticus_Prdm1 fl/fl Maf fl/fl,2


title: Prdm1fl/fl Maf fl/fl  Cd4Cre_Infected.3

description:
10x Genomics v3.1
ALV5070A12

value: Prdm1fl/fl Maf fl/fl  Cd4Cre


title: COX2453A1,H. hepaticus_Prdm1 fl/fl Maf fl/fl,1


title: 1_shNT_CD133-


title: Prdm1fl/fl Maf fl/fl_Infected.3

description:
10x Genomics v3.1
ALV5070A11

value: Prdm1fl/fl Maf fl/fl


title: Prdm1fl/fl Maf fl/fl_Uninfected.2

description:
10x Genomics v3.1
ALV5070A9

value: Uninfected


title: Prdm1fl/fl Maf fl/fl  Cd4Cre_Uninfected.2

description:
10x Genomics v3.1
ALV5070A10


title: 1_shNT_CD133p

value: HEC-1A endomertial cell line was infected with shGFP (shNT) as control. The control cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations.


title: Prdm1fl/fl Maf fl/fl_Infected.2

description:
10x Genomics v3.1
ALV5070A7


title: Prdm1fl/fl Maf fl/fl  Cd4Cre_Infected.2

description:
10x Genomics v3.1
ALV5070A8


title: COX2453A29,Uninfected_Prdm1 fl/fl Maf fl/fl CD4-Cre,2

value: Prdm1 fl/fl Maf fl/fl CD4-Cre


title: COX2453A30,Uninfected_Prdm1 fl/fl Maf fl/fl CD4-Cre,3


title: Maf fl/fl  Cd4Cre_Infected.1

description:
10x Genomics v3.1
ALV5070A6


title: 1_shDAP5_CD133p


title: GT3aOE_Pto_rep3

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

institute: Kyoto university

data_processing:
Reads were quality filtered by fastp (ver. 0.19.7) with the parameters -x -f 8 -q 30 -b 50.
Arabidopsis genome indexes were generated by STAR (ver. 2.6.1b) using the the paremeters --runMode genomeGenerate --genomeDir /home/user/ngs/data1/At_genome_sjdbOverhang139/ --genomeFastaFiles Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --sjdbGTFfile Arabidopsis_thaliana.TAIR10.34.gtf --sjdbOverhang 139 --runThreadN 8
Reads were mapped by STAR (ver. 2.6.1b) with the default parameters and transformed to a count per gene per library by featureCounts (ver. 1.6.0) with the parameters -s 1 -t exon -g gene_id
Supplementary files format and content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
RNA was isolated using TRI Reagent (Sigma). One mg of total RNA was used for library preparation.
BrAD-seq (Townley et al., 2015, doi: 10.3389/fpls.2015.00366.)

value: Leaf

value: Pto

tag: replicate


title: COX2453A28,Uninfected_Prdm1 fl/fl Maf fl/fl CD4-Cre,1


title: 1_shDAP5_CD133-

value: HEC-1A endomertial cell line was KD with shRNA for EIF4G2 (DAP5) . The  cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations.


title: Prdm1fl/fl Maf fl/fl  Cd4Cre_Infected.1

description:
10x Genomics v3.1
ALV5070A4

value: colon lamina propria


title: Col_Pto_rep3


title: COX2453A25,Uninfected_Prdm1 fl/fl Maf fl/fl,3

value: sorted CD4+ T cells


title: GT3aOE_mock_rep3

value: Mock


title: Prdm1fl/fl Cd4Cre_Infected.1

description:
10x Genomics v3.1
ALV5070A5

value: colon LPL


title: HCC827 CBX5 shRNA2 [CBX5g7_2]

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description:
HCC827 CBX5 shRNA2 replicate 2
8_08JP_016OUAB_H_ATAC_hs_i227

data_processing:
ATAC-Seq libraries were sequenced on Illumina NextSeq 500 as 42-nt paired end reads.
Pre-alignment quality assessments of the raw fastq sequences were performed using FastQC(v0.11.9)(Andrews, 2010). TrimGalore(v0.6.4_dev) was used to remove adapter from the reads. The pre-processed fastq reads were aligned to the human hg38 reference genome (GenBank assembly accession: GCA_000001405.28) using BWA(v0.7.17-r1188)(Li & Durbin 2010). Duplicates were marked with Picard(v2.23.1). Reads with the following criterion were filtered out: reads that map to mitochondrial DNA (SAMTools)(v1.10) (Li et al 2009); reads marked as duplicates (SAMTools)(v1.10); reads that are not primary alignments (SAMTools)(v1.10); reads that are unmapped (SAMTools)(v1.10); reads that map to multiple locations (SAMTools)(v1.10); reads containing > 4 mismatches (BAMTools)(v2.29.2) (Barnett et al 2011); reads that are soft-clipped (BAMTools)(v2.29.2); reads with an insert size > 2kb (BAMTools)(v2.29.2); reads that map to different chromosomes (SAMTools)(v1.10)(Li et al 2009); reads that are not in the FR orientation (SAMTools)(v1.10); reads with only one read of the pair fails the above criteria (SAMTools)(v1.10). Broad peaks were called with MACS2 (v2.2.7.1)(Zhang et al 2008).
Genome_build: human hg38 reference genome
Supplementary_files_format_and_content: broadPeak is a BED 6+3 format (http://genome.ucsc.edu/FAQ/FAQformat.html#format13)

source_name: HCC827 CBX5 shRNA2

growth_protocol: HCC827 cells stably expressing either CBX5 shRNAs or NS shRNA were grown in RPMI1640 medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were thawed in a 37oC water bath, pelleted, washed with cold PBS. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter)

tag: genotype/variation

value: expressing CBX5 shRNAs


title: Prdm1fl/fl Maf fl/fl_Infected.1

description:
10x Genomics v3.1
ALV5070A3

value: Infected


title: COX2453A24,Uninfected_Prdm1 fl/fl Maf fl/fl,2

value: Prdm1 fl/fl Maf fl/fl


title: HCC827 CBX5 shRNA2 [CBX5g7_3]

description:
HCC827 CBX5 shRNA2 replicate 3
9_08JQ_016OUAB_I_ATAC_hs_i228


title: Col_mock_rep3


title: Prdm1fl/fl Maf fl/fl  Cd4Cre_Uninfected.1

description:
10x Genomics v3.1
ALV5070A2


title: GT3aOE_Pto_rep2


title: HCC827 CBX5 shRNA2 [CBX5g7_1]

description:
HCC827 CBX5 shRNA2 replicate 1
7_08JO_016OUAB_G_ATAC_hs_i226


title: Col_Pto_rep2


title: COX1204A37_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl CD4-Cre

description:
RNA_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl CD4-Cre
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 genome and the GENCODE reference transcriptome version M22 with STAR software
Raw gene counts were retrieved using QoRTs software
Normalised read counts were retrieved using DeSeq2
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided  for RNA-seq data separated for both strands and normalised to RPKMs

source_name: colon LPL from mice with the treatment: Hhepaticus_antiIL-10R

extract_protocol:
On Day 14 following infection with Helicobacter hepaticus, colon lamina propria leukocytes were isolated from individual  infected and uninfected control mice. RNA was extracted using the QIAShredder and RNeasy Mini Kit with on-column DNase digestion, according to the manufacturer’s instructions (Qiagen).
RNA-seq libraries were made with total RNA using the KAPA RNA HyperPrep with RiboErase and unique multiplexing indexes, according to the manufacturer’s instructions (Roche).

treatment_protocol: Mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: prdm1 fl/fl maf fl/fl CD4-Cre

value: LPL from mice treated with Hhepaticus_antiIL-10R


title: GT3aOE_mock_rep2


title: HCC827 CBX5 shRNA1 [CBX5g1_3]

description:
HCC827 CBX5 shRNA1 replicate 3
6_08JN_016OUAB_F_ATAC_hs_i225

source_name: HCC827 CBX5 shRNA1


title: HCC827 CBX5 shRNA1 [CBX5g1_2]

description:
HCC827 CBX5 shRNA1 replicate 2
5_08JM_016OUAB_E_ATAC_hs_i224


title: COX1204A36_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl CD4-Cre


title: Prdm1fl/fl Maf fl/fl_Uninfected.1

description:
10x Genomics v3.1
ALV5070A1


title: COX2453A23,Uninfected_Prdm1 fl/fl Maf fl/fl,1


title: COX1204A35_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl CD4-Cre


title: COX1204A34_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl CD4-Cre


title: HCC827 NSshRNA [NS_3]

description:
HCC827 NSshRNA Replicate 3
3_08JK_016OUAB_C_ATAC_hs_i222

source_name: HCC827 NSshRNA

value: expressing control shRNA


title: GT3aOE_Pto_rep1


title: HCC827 NSshRNA [NS_2]

description:
HCC827 NSshRNA Replicate 2
2_08JJ_016OUAB_B_ATAC_hs_i221


title: COX1204A33_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl CD4-Cre


title: Col_Pto_rep1


title: GT3aOE_mock_rep1


title: COX1204A45_Hhepaticus_antiIL-10R_maf fl/fl CD4-Cre

description:
RNA_Hhepaticus_antiIL-10R_maf fl/fl CD4-Cre
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: maf fl/fl CD4-Cre


title: COX1204A44_Hhepaticus_antiIL-10R_maf fl/fl CD4-Cre


title: COX1204A43_Hhepaticus_antiIL-10R_maf fl/fl CD4-Cre


title: Col_mock_rep1


title: mmyRNAi_2

city: Hangzhou

first: Yue

state: Zhejiang

address: The College of Medicine Keyan C-161, Zijingang Campus, Zhejiang University, Yuhangtang Rd. 866

department: School of medicine

institute: Zhejiang University

data_processing:
The clean reads were mapped to the Drosophila genome sequence using Hisat2 with default parameters.
The number of mapped reads were counted by featureCounts.
Differential gene expression analysis was performed using the DESeq2 package. Adjusted p-value < 0.05 was used as the threshold to identify the differentially expressed genes.
Assembly: dm6
Supplementary files format and content: Excel file "counts_control_mmyRNAi.xlsx" of raw counts for each sample.
Supplementary files format and content: Excel file "mmyRNAi.xlsx" after DESeq2 for each sample.

organism: Drosophila melanogaster

source_name: tracheal progenitors in white pupae

extract_protocol:
The white pupae were dissected in cold PBS and a single cluster of progenitors from Tr5 metamere were subjected to RNA extraction using the RNeasy Micro Kit from Qiagen. Total RNA from each sample was used for sequencing library preparation. Three biological replicates were performed for each genotype or treatment.
The SMART-Seq v4 Ultra low input RNA Kit was used for first-strand and second strand cDNA synthesis and double-stranded cDNA end repair. Double strand cDNAs were purified using the AMPure XP from Beckman Coulter, subjected to tagmentation and ligated to adaptors. Finally, the libraries were generated by PCR enrichment of the adaptor-ligated DNA.

value: tracheal progenitors in white pupae

value: normal diet


title: mmyRNAi_3


title: mmyRNAi_1


title: Col_mock_rep2


title: COX1204A42_Hhepaticus_antiIL-10R_prdm1 fl/fl CD4-Cre

description:
RNA_Hhepaticus_antiIL-10R_prdm1 fl/fl CD4-Cre
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: prdm1 fl/fl CD4-Cre


title: control_2


title: HCC827 CBX5 shRNA1 [CBX5g1_1]

description:
HCC827 CBX5 shRNA1 replicate 1
4_08JL_016OUAB_D_ATAC_hs_i223


title: COX1204A41_Hhepaticus_antiIL-10R_prdm1 fl/fl CD4-Cre


title: control_3


title: 51.5.4 vehicle

type: protein

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Straße 53

department: Interdisziplinäres Tumorzentrum

institute: University Medical Center Freiburg

description:
180-205 28
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody

hyb_protocol: sample is pumped through porous membrane

scan_protocol: when the solution is underneath the array, images are taken at several exposure times

data_processing: images are used by the BioNavigator software to calculate signal values for each phosphosite.

label: fluorescently labelled anti phospho antibody

molecule: protein

source_name: BMDMs

label_protocol: maximum 15 µl was used as per proprietary protocol of PamGene

growth_protocol: Bone marrow was isolated from five wild-type C57BL/6 mice, erythrocytes were lyzed and residual cells were plated in RPMI+10%FCS+1%PenStrep+20ng/ml rmCSF at 3.5x10^6 cells per 10cm dish. Cells were cultivated until d7, when they were treated with LPS and IFNg. 16 hours after stimulation, cell pellets were harvested.

extract_protocol: Cell pellets were frozen, shipped, and lyzed in 25 µl buffer with protease and phosphatase inhibitors.

treatment_protocol: From start of differentiation, cells were kept with 150 ng/ml LCN2 or vehicle.

value: bone marrow derived macrophages

value: C57BL/6 wildtype

tag: gender

value: female

tag: treament

value: vehicle


title: COX1204A40_Hhepaticus_antiIL-10R_prdm1 fl/fl CD4-Cre


title: 51.4.1 vehicle

description:
180-205 29
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody

tag: genotype


title: 51.5.4 LCN2

description:
180-205 34
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody

tag: cell type


title: HSD, scRNAseq

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made by Cell Rager-6.1.2.
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: trachea in white pupae

extract_protocol:
About 100 trachea of pupae were dissected in cold Grace medium supplemented with 2.5% fly extract, 1mM PMSF and EDTA-free protease inhibitor cocktail (Roche) within 1 hour and digested in 1 mg /ml Elastase (Sigma, #E0258) solution at 25℃ for 1 hr.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: trachea in white pupae

tag: treatment

value: high surgar diet


title: COX1204A39_Hhepaticus_antiIL-10R_prdm1 fl/fl CD4-Cre


title: control_1


title: COX1204A38_Hhepaticus_antiIL-10R_prdm1 fl/fl CD4-Cre


title: 51.4.4 LCN2

description:
180-205 38
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody


title: 51.4.4 vehicle

description:
180-205 32
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody


title: HCC827 NSshRNA [NS_1]

description:
HCC827 NSshRNA Replicate 1
1_08JI_016OUAB_A_ATAC_hs_i220

tag: cell line


title: maternal HFD_female offspring, replicate2, snRNA-seq

city: Shenzhen

first: John

middle: R.

last: Speakman

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

description:
10x Genomics
m48f

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
qc, normalization, dimentional reduction, integration and clustering were processed in Seurat
Assembly: mm10
Supplementary files format and content: processed (qc'ed, integrated and subsetted) rds file

source_name: hypothalamus

extract_protocol:
Male and female pup brains were rapidly dissected between 9 and 12 a.m., hypothalamus was spooned out immediately and cut into tiny pieces in HEB buffer (Hibernate A®, 2% B27®, 0.5mM GlutaMAXTM). Hypothalamus pieces were then incubated in 2 ml pre-chilled lysis buffter (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 Substitute in Nuclease-Free Water, 0.1U/μl RNase Inhibitor) on ice for 15 min. Added 2ml HEB buffer to the lysed tissue and triturated the tissue with a fire polished silanized Pasteur pipette 10–15 times. After trituration, a 30 μm MACS® SmartStrainer was used to remove cell debris and large clumps. The single nucleus suspension was centrifuged at 400g for 5min at 4°C and washed in a wash and resuspension buffer (1X PBS with 1.0% BSA and 0.2U/μl RNase Inhibitor).
Library was constructed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
snRNA-seq

treatment_protocol: Female C57BL/6N mice at 11 weeks of age were fed with low fat diets (10% fat by energy) for 2 weeks of baseline. Mice were mated at 13 weeks old and remained on LFD until parturition. Mice were then randomly allocated to low fat diets and high fat diets (45% fat by energy) on lactation day 1 and kept feeding them those diets during the lactation.

value: neuronal, non-neuronal, and immune cells

value: hypothalamus

value: postnatal day15

tag: Sex

tag: maternal diet

value: HFD


title: ND, scRNAseq

tag: tissue


title: COX1204A32_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl

description:
RNA_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: prdm1 fl/fl maf fl/fl


title: maternal HFD_female offspring, replicate1, snRNA-seq

description:
10x Genomics
m6f

tag: age


title: 51.4.3 LCN2

description:
180-205 37
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody


title: maternal HFD_male offspring, replicate2, snRNA-seq

description:
10x Genomics
m71m

value: male


title: 51.4.3 vehicle

description:
180-205 31
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody


title: 51.4.1 LCN2

description:
180-205 35
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody


title: maternal HFD_male offspring, replicate1, snRNA-seq

description:
10x Genomics
m50m