title: embryo, wild type for HIRA mislocalized mutant, 2.5-3h, rep2

description: 2.5_3h_embryo_wild_type_for_HIRA_mislocalized_mutant_RNAseq_replicate_2


title: IN_6_P

status: Public on Nov 14 2024

type: SRA

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

country: China

library_source: transcriptomic

data_processing:
Sequencing was carried out using Illumina NovaSeq 6000 with 150 bp paired-end reads. Gene expression level analysis was performed using R (Version 4.3.1) package Seurat (Version 5.0.2), and the mean gene expression matrix of all samples was obtained after processing by NormalizeData function. For marker gene analysis of each subpopulation, FindAllMarkers function in Seurat was used, with parameters set as min.pct=0.1 and logfc.threshold=0.25.
Assembly: danRer11
Supplementary files format and content: Excel file include readcounts values for each Sample.

molecule: total RNA

organism: Danio rerio

source_name: brain

growth_protocol: Tg(tph2:GFP) fish at 7 dpf were used.

extract_protocol:
For each sample, 10-12 neurons were collected and transferred to lysis buffer solution. Total RNA was extracted for construction of cDNA libraries, involving fragmentation, PCR enrichment, N7 index linking, and purification.
A total of 71 QuantSeq libraries (N=9-12 samples for each subpopulation) were prepared using the Lexogen’s QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution. The somata of 5-HT neurons from seven subpopulations (PT, SR-R, SR-M, SR-C, IR-R, IR-C, MO) were visualized under a fluorescence microscopy, then targeted and collected separately using glass electrode.

tag: tissue

value: brain

tag: strain

tag: cell type

value: 5-HT neurons

tag: developmental stage


title: embryo, M-Z+ HIRA mutant, 2.5-3h, rep 1

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

description: 2.5-3h_embryo_M-Z+_HIRA_mutant_RNAseq_replicate_1

data_processing:
Sequence reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to dm6 using STAR (v2.7.10a).
Read count extraction were performed using RSEM (v1.3.1).
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.40.2).
Assembly: dm6
Supplementary files format and content: tab-delimited text files include gene expression for each Sample.

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
Total RNAs were extracted from embryos at specific stages utilizing TRIzol reagent. Each RNA sample (0.5 µg total RNA) underwent rRNA depletion.
Strand-specific libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI, following the manufacturer's instructions.

value: embryo

tag: genotype

value: M-Z+ HIRA mutant

tag: time point


title: embryo, HIRA mislocalized mutant, 2.5-3h, rep2

description: 2.5_3h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_2

value: HIRA mislocalized mutant


title: C_DRN_13


title: embryo, M-Z+ HIRA mutant, 2.5-3h, rep 2

description: 2.5-3h_embryo_M-Z+_HIRA_mutant_RNAseq_replicate_2


title: embryo, HIRA mislocalized mutant, 2.5-3h, rep1

description: 2.5_3h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: embryo, wild type for HIRA mislocalized mutant, 2.5-3h, rep1

description: 2.5_3h_embryo_wild_type_for_HIRA_mislocalized_mutant_RNAseq_replicate_1

value: wild type


title: embryo, M-Z+ HIRA mutant, 160-190min, rep2

description: 160-190min_embryo_M-Z+_HIRA_mutant_RNAseq_replicate_2


title: embryo, HIRA mislocalized mutant, 160-190min, rep2

description: 160_190min_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_2


title: embryo, wild type for HIRA mislocalized mutant, 1-1.5h, rep2

description: 1_1.5h_embryo_wild_type_for_HIRA_mislocalized_mutant_RNAseq_replicate_2


title: embryo, M-Z+ HIRA mutant, 160-190min, rep1

description: 160-190min_embryo_M-Z+_HIRA_mutant_RNAseq_replicate_1


title: embryo, wild type for HIRA mislocalized mutant, 1-1.5h, rep1

description: 1_1.5h_embryo_wild_type_for_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: embryo, HIRA mislocalized mutant, 1-1.5h, rep2

description: 1_1.5h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_2


title: embryo, wild type for HIRA mislocalized mutant, 0.5-1h, rep1

description: 0.5_1h_embryo_wild_type_for_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: embryo, wild type for HIRA mislocalized mutant, 0.5-1h, rep2

description: 0.5_1h_embryo_wild_type_for_HIRA_mislocalized_mutant_RNAseq_replicate_2


title: embryo, HIRA mislocalized mutant, 160-190min, rep1

description: 160_190min_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: embryo, M-Z+ HIRA mutant, 5.5-6h, rep2

description: 5.5-6h_embryo_M-Z+_HIRA_mutant_RNAseq_replicate_2


title: C_DRN_2


title: embryo, HIRA mislocalized mutant, 1-1.5h, rep1

description: 1_1.5h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: C_DRN_6


title: embryo, HIRA mislocalized mutant, 0.5-1h, rep1

description: 0.5_1h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_1


title: embryo, wild type for nosPmyc HIRA, GAF, ChIP, 0.5-1.5h, rep1

description: 0.5-1.5h_embryo_wild_type_for_nosPmyc_HIRA_GAF_CHIPseq_replicate_1

library_source: genomic

data_processing:
Paired-end reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to mapped to Drosophila melanogaster (dm6) using bowtie2 (v2.2.5).
PCR duplicates were marked using sambamba (v0.8.2). Non-uniquely mapped reads, low-quality reads (quality scores less than 30) were removed using samtools (v1.18).
Bigwig files were generated from resulting deduplicated and filtered bam files using deeptools (v3.5.1).
Assembly: dm6
Supplementary files format and content: BigWig

molecule: genomic DNA

extract_protocol:
The embryos of indicated genotypes were harvested and subjected to cross-linking by fixation buffer (50 mM HEPES, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl and 1.8% formaldehyde). They were cross-linked for 20 minutes and then quenched with 125 mM glycine (final concentration) for 5 minutes at room temperature. Chromatin immunoprecipitation (ChIP) reactions were carried out in duplicate using the Pierce Magnetic ChIP Kit and the following antibodies: mouse anti-dPCIF1 (1:100), mouse anti-GAF (1:100), mouse anti-Zelda (1:100), mouse anti-HIRA (1:100), rabbit anti-RNA polymerase II-phospho S5 (1:200).
Sequencing libraries were generated using the VAHTS Universal DNA Library Prep Kit for MGI.

tag: chip antibody

value: GAF


title: embryo, wild type for nosPmyc HIRA, GAF, ChIP, 0.5-1.5h, rep2

description: 0.5-1.5h_embryo_wild_type_for_nosPmyc_HIRA_GAF_CHIPseq_replicate_2


title: embryo, wild type for nosPmyc HIRA, GAF, ChIP input, 0.5-1.5h, rep2

description: 0.5-1.5h_embryo_wild_type_for_nosPmyc_HIRA_GAF_CHIPseq_input_replicate_2


title: embryo, wild type for nosPmyc HIRA, GAF, ChIP input, 0.5-1.5h, rep1

description: 0.5-1.5h_embryo_wild_type_for_nosPmyc_HIRA_GAF_CHIPseq_input_replicate_1


title: embryo, wild type for HIRA mutant, GAF, ChIP, 2-3h, rep1

description: 2-3h_embryo_wild_type_for_HIRA_mutant_GAF_CHIPseq_replicate_1


title: embryo, wild type for HIRA mutant, GAF, ChIP, 2-3h, rep2

description: 2-3h_embryo_wild_type_for_HIRA_mutant_GAF_CHIPseq_replicate_2


title: embryo, wild type for HIRA mutant, GAF, ChIP input, 2-3h, rep1

description: 2-3h_embryo_wild_type_for_HIRA_mutant_GAF_CHIPseq_input_replicate_1


title: embryo, nosPmyc HIRA, GAF, ChIP, 0.5-1.5h, rep2

description: 0.5-1.5h_embryo_nosPmyc_HIRA_GAF_CHIPseq_replicate_2

value: nosPmyc HIRA


title: embryo, nosPmyc HIRA, GAF, ChIP input, 0.5-1.5h, rep2

description: 0.5-1.5h_embryo_nosPmyc_HIRA_GAF_CHIPseq_input_replicate_2


title: embryo, nosPmyc HIRA, GAF, ChIP input, 0.5-1.5h, rep1

description: 0.5-1.5h_embryo_nosPmyc_HIRA_GAF_CHIPseq_input_replicate_1


title: embryo, M-Z+ HIRA mutant, GAF, ChIP, 2-3h, rep1

description: 2-3h_embryo_M-Z+_HIRA_mutant_GAF_CHIPseq_replicate_1


title: embryo, wild type for dPCIF1 S111A S115A, 1-1.5h, rep2

data_processing:
Sequence reads were trimmed by trimmomatic (v0.39)
Clean reads were mapped to dm6 using STAR (v2.7.10a)
Read count extraction were performed using RSEM (v1.3.1)
Reads normalization and differentially-expressed gene calling were performed using DESeq2 (v1.40.2)
Assembly: dm6
Supplementary files format and content: tab-delimited text files include gene expression for each Sample

molecule: polyA RNA

extract_protocol:
Total RNAs were extracted from embryos at specific stages utilizing TRIzol reagent.  Each RNA sample (0.5 µg total RNA) underwent rRNA depletion.
Strand-specific libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI, following the manufacturer's instructions.


title: embryo, M-Z+ HIRA mutant, GAF, ChIP input, 2-3h, rep2

description: 2-3h_embryo_M-Z+_HIRA_mutant_GAF_CHIPseq_input_replicate_2


title: embryo, wild type for dPCIF1 S111A S115A, 1-1.5h, rep1


title: embryo, M-Z+ HIRA mutant, GAF, ChIP input, 2-3h, rep1

description: 2-3h_embryo_M-Z+_HIRA_mutant_GAF_CHIPseq_input_replicate_1


title: embryo, dPCIF1 S111A S115A, 1-1.5h, rep2

value: dPCIF1 S111A S115A


title: embryo, HIRA mislocalized mutant, 0.5-1h, rep2

description: 0.5_1h_embryo_HIRA_mislocalized_mutant_RNAseq_replicate_2


title: embryo, M-Z+ HIRA mutant, GAF, ChIP, 2-3h, rep2

description: 2-3h_embryo_M-Z+_HIRA_mutant_GAF_CHIPseq_replicate_2


title: embryo, wild type for dPCIF1 S111A S115A, 0.5-1h, rep1


title: embryo, nosPmyc HIRA, GAF, ChIP, 0.5-1.5h, rep1

description: 0.5-1.5h_embryo_nosPmyc_HIRA_GAF_CHIPseq_replicate_1


title: embryo, dPCIF1 S111A S115A, 1-1.5h, rep1


title: embryo, wild type for overexpression, 1-1.5h, rep1


title: embryo, wild type for overexpression, 1-1.5h, rep2


title: embryo, overexpression HIRA and dPCIF1, 1-1.5h, rep1

value: overexpression HIRA and dPCIF1


title: embryo, overexpression HIRA, 1-1.5h, rep2

value: overexpression HIRA


title: embryo, dPCIF1 S111A S115A, 0.5-1h, rep1


title: embryo, overexpression HIRA, 1-1.5h, rep1


title: embryo, wild type for dPCIF1 S111A S115A, 0.5-1h, rep2


title: embryo, wild type for HIRA mutant, GAF, ChIP input, 2-3h, rep2

description: 2-3h_embryo_wild_type_for_HIRA_mutant_GAF_CHIPseq_input_replicate_2


title: embryo, wild type for overexpression, 0.5-1h, rep2


title: embryo, overexpression HIRA and dPCIF1, 1-1.5h, rep2


title: embryo, overexpression HIRA and dPCIF1, 0.5-1h, rep2


title: embryo, overexpression HIRA and dPCIF1, 0.5-1h, rep1


title: embryo, overexpression HIRA, 0.5-1h, rep2


title: embryo, overexpression HIRA, 0.5-1h, rep1


title: embryo, wild type for H3.3 mutant, 2.5-3h, rep2


title: embryo, wild type for H3.3 mutant, 2.5-3h, rep1


title: embryo, M-Z+ H3.3 mutant, 2.5-3h, rep2

value: M-Z+ H3.3 mutant


title: embryo, dPCIF1 S111A S115A, 0.5-1h, rep2


title: embryo, wild type for H3.3 mutant, 1-1.5h, rep1


title: embryo, M-Z+ H3.3 mutant, 1-1.5h, rep1


title: embryo, wild type for H3.3 mutant, 0.5-1h, rep2


title: embryo, wild type for H3.3 mutant, 0.5-1h, rep1


title: embryo, M-Z+ H3.3 mutant, 1-1.5h, rep2


title: embryo, M-Z+ H3.3 mutant, 0.5-1h, rep2


title: embryo, M-Z+ H3.3 mutant, 0.5-1h, rep1


title: embryo, wild type for HIRA mutant, 2.5-3h, rep2


title: embryo, wild type for HIRA mutant, 2.5-3h, rep1


title: embryo, wild type for HIRA mutant, 1-1.5h, rep2


title: embryo, M-Z+ HIRA mutant, 2.5-3h, rep1


title: embryo, wild type for overexpression, 0.5-1h, rep1


title: embryo, wild type for HIRA mutant, 1-1.5h, rep1


title: embryo, wild type for HIRA mutant, 0.5-1h, rep2


title: embryo, M-Z+ HIRA mutant, 1-1.5h, rep1


title: embryo, M-Z+ HIRA mutant, 1-1.5h, rep2


title: embryo, M-Z+ HIRA mutant, 2.5-3h, rep2


title: embryo, M-Z+ HIRA mutant, 0.5-1h, rep2


title: embryo, M-Z+ HIRA mutant, 0.5-1h, rep1


title: embryo, wlid type for dPCIF1 mutant, 1-1.5h, rep2


title: embryo, dPCIF1 mislocalized mutant, 1-1.5h, rep2

value: dPCIF1 mislocalized mutant


title: embryo, wild type for HIRA mutant, 0.5-1h, rep1


title: embryo, wild type for H3.3 mutant, 1-1.5h, rep2


title: embryo, wlid type for dPCIF1 mutant, 0.5-1h, rep2


title: embryo, M-Z+ H3.3 mutant, 2.5-3h, rep1


title: embryo, dPCIF1 mislocalized mutant, 1-1.5h, rep1


title: embryo, wlid type for dPCIF1 mutant, 0.5-1h, rep1


title: embryo, dPCIF1 mislocalized mutant, 0.5-1h, rep2


title: embryo, dPCIF1 mislocalized mutant, 0.5-1h, rep1


title: embryo, M-Z+ dPCIF1 mutant, GAF ZLD, ChIP input, 0.5-1.5h, rep2

data_processing:
Paired-end reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to mapped to Drosophila melanogaster (dm6) using bowtie2 (v2.2.5).
PCR duplicates were marked using sambamba (v0.8.2).Non-uniquely mapped reads, low-quality reads (quality scores less than 30) were removed using samtools (v1.18).
Peaks were calculated using macs2 (v2.2.7.1) with a q-value cutoff of 0.01
Bigwig files were generated from resulting deduplicated and filtered bam files using deeptools (v3.5.1).
Assembly: dm6
Supplementary files format and content: BigWig, narrowPeak (except for Input sample)

extract_protocol:
The embryos of indicated genotypes were harvested and subjected to cross-linking by fixation buffer (50 mM HEPES, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl and 1.8% formaldehyde).  They were cross-linked for 20 minutes and then quenched with 125 mM glycine (final concentration) for 5 minutes at room temperature.  Chromatin immunoprecipitation (ChIP) reactions were carried out in duplicate using the Pierce Magnetic ChIP Kit and the following antibodies: mouse anti-dPCIF1 (1:100), mouse anti-GAF (1:100), mouse anti-Zelda (1:100), mouse anti-HIRA (1:100), rabbit anti-RNA polymerase II-phospho S5 (1:200).
Sequencing libraries were generated using the VAHTS Universal DNA Library Prep Kit for MGI.

value: M-Z+ dPCIF1 mutant


title: embryo, M-Z+ dPCIF1 mutant, GAF ZLD, ChIP input, 0.5-1.5h, rep1


title: embryo, wlid type for dPCIF1 mutant, 1-1.5h, rep1


title: embryo, M-Z+ dPCIF1 mutant, ZLD, ChIP, 0.5-1.5h, rep2

value: ZLD


title: embryo, M-Z+ dPCIF1 mutant, ZLD, ChIP, 0.5-1.5h, rep1


title: embryo, M-Z+ dPCIF1 mutant, GAF, ChIP, 0.5-1.5h, rep1


title: embryo, wild type, GAF ZLD, ChIP input, 0.5-1.5h, rep1


title: embryo, wild type, GAF ZLD, ChIP input, 0.5-1.5h, rep2


title: embryo, wild type, GAF, ChIP, 0.5-1.5h, rep2


title: embryo, wild type, ZLD, ChIP, 0.5-1.5h, rep1


title: embryo, wild type, GAF, ChIP, 0.5-1.5h, rep1


title: embryo, wild type, POLII-Ser5P, ChIP input, 0.5-1.5h, rep1


title: embryo, wild type, POLII-Ser5P, ChIP, 0.5-1.5h, rep2


title: embryo, wild type, HIRA, ChIP, 0.5-1.5h, rep2

value: HIRA


title: embryo, wild type, ZLD, ChIP, 0.5-1.5h, rep2


title: embryo, wild type, HIRA, ChIP input, 0.5-1.5h, rep2


title: embryo, wild type, dPCIF1, ChIP input, 0.5-1.5h, rep2


title: embryo, wild type, POLII-Ser5P, ChIP, 0.5-1.5h, rep1


title: embryo, wild type, POLII-Ser5P, ChIP input, 0.5-1.5h, rep2


title: embryo, wild type, HIRA, ChIP, 0.5-1.5h, rep1


title: embryo, wild type, HIRA, ChIP input, 0.5-1.5h, rep1


title: embryo, wild type, dPCIF1, ChIP, 0.5-1.5h, rep1


title: embryo, wild type, dPCIF1, ChIP, 0.5-1.5h, rep2


title: embryo, wild type, dPCIF1, ChIP input, 0.5-1.5h, rep1


title: embryo, M-Z+ dPCIF1 mutant, GAF, ChIP, 0.5-1.5h, rep2


title: embryo, wild type for HIRA mutant, ATAC, 0.5-1.5h, rep1

data_processing:
Paired-end reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to mapped to Drosophila melanogaster (dm6) using bowtie2 (v2.2.5).
PCR duplicates were marked using sambamba (v0.8.2).Non-uniquely mapped reads, low-quality reads (quality scores less than 30) were removed using samtools (v1.18).
Peaks were calculated using macs2 (v2.2.7.1) with a q-value cutoff of 0.01
Bigwig files were generated from resulting deduplicated and filtered bam files using deeptools (v3.5.1).
Assembly: dm6
Supplementary files format and content: BigWig, narrowPeak

extract_protocol:
The embryos of indicated genotypes were harvested and dechorionated in 50% commercial bleach solution.  Subsequently, the embryos were resuspended with ATAC-lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) and homogenized with a loose stroke 50 times, followed by centrifugation at 500 g for 5 minutes to pellet the nuclei at 4℃.
The ATAC-seq libraries of embryos were prepared using the TruePrep DNA Library Prep Kit for MGI.


title: embryo, M-Z+ HIRA mutant, ATAC, 0.5-1.5h, rep1


title: embryo, M-Z+ HIRA mutant, ATAC, 2-3h, rep2


title: embryo, wild type for dPCIF1 mutant, ATAC, 0.5-1.5h, rep1


title: embryo, wild type for HIRA mutant, ATAC, 0.5-1.5h, rep2


title: embryo, M-Z+ dPCIF1 mutant, ATAC, 0.5-1.5h, rep1


title: embryo, M-Z+ dPCIF1 mutant, ATAC, 0.5-1.5h, rep2


title: embryo, M-Z+ HIRA mutant, ATAC, 2-3h, rep1


title: embryo, wild type for HIRA mutant, ATAC, 2-3h, rep2


title: embryo, wild type for HIRA mutant, ATAC, 2-3h, rep1


title: embryo, wild type for dPCIF1 mutant, ATAC, 0.5-1.5h, rep2


title: RUNX2, Memory, PostCAR, Exp2, TR1

city: Denver

first: James

last: Scott-Browne

state: Colorado

address: 1400 Jackson St, K806

country: USA

institute: National Jewish Health

description: Memory-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq.
Fastq files were used to map to the mm10 genome using the ENCODE ATAC-seq pipeline, with default parameters, except bam files used for peak calling were randomly downsampled to a maximum of 50 million mapped reads.
Peaks with a MACS2 computed q value of less than 0.0001  in at least one replicate were merged with bedtools function intersect and processed to uniform peaks with the functions getPeaks and resize from R package ChromVAR.
Reads overlapping peaks were enumerated with getCounts function from ChromVAR and normalized and log2-transformed with voom from R package limma.
Peaks with 6 or more normalized counts per million mapped reads at least one replicate were included to define a global peak set of 99,317 peaks .
Assembly: mm10
Supplementary files format and content: bigwig of individual replicates

organism: Mus musculus

source_name: Splenic T cells

growth_protocol: CD8+ T cells were maintained in RPMI1640 media supplemented with L-Glutamine, non-essential amino acids, sodium pyruvate, HEPES, antibiotics and 10% FBS.

extract_protocol:
For ATACseq, cells were processed using the Omni-ATAC protocol. Sorted cells were washed once in 1X PBS, lysed, washed once in Wash Buffer and then the transposition reaction was carried out at 32°C for 30 minutes on a thermomixer set to 1000 rpm. Transposed chromatin was then purified using the Zymo Clean and Concentrator 5 Kit using manufacturer protocols.
DNA was then ran on PCR for 12 total cycles with dual-index barcoding primers. PCR reactions were then size-selected using AMPure XP beads and checked for quality and size distribution using TapeStation 4200 with D5000 reagents. Libraries were pooled at equimolar ratios for sequencing.

treatment_protocol: Vaccination was carried out with whole ovalbumin protein, anti-mouse CD40 and PolyI:C, with concurrent adoptive transfer of 5000 OT-I CD8+ T cells. OT-I T cells were isolated from vaccinated mice on day 28 post-vaccination from pooled vaccinated hosts (memory), or age-matched naïve mice (naïve). CD8+ T cells were activated using anti-CD3/anti-CD28 Dynabeads in the presence of IL-2 and IL-7, and transduced with a murine anti-mouse CD19 CAR containing CD28 costimulatory domain and CD3zeta domain and either pMSCV-mRUNX2-IRES-eGFP or empty pMSCV-IRES-eGFP.

value: Splenic T cells

value: CD8+ T cell

value: Rag2-/- OT-I TCR transgenic

tag: treatment


title: embryo, M-Z+ HIRA mutant, ATAC, 0.5-1.5h, rep2

value: embryo


title: Memory, PostCAR, Exp2, TR1

value: CAR+Vaccine


title: RUNX2, Naïve, PostCAR, Exp2, TR1

description: Naïve-derived CD8+/CAR+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: Memory, PostCAR, Exp1, TR1

description: Memory-derived CD8+/CAR+/GFP+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: RUNX2, Naïve, PostCAR, Exp1, TR1

description: Naïve-derived CD8+/CAR+/GFP+ T cells were collected in vitro after 5 day CAR-transduction protocol.


title: Naïve, PostCAR, Exp2, TR3

city: Aurora

first: Terry

last: Fry

state: CO

institute: University of of Colorado Denver and Children's Hospital Col

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq.
Quality of fastq files was accessed using FastQC (v.0.11.8) , FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the mm10 murine reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a).
Assembly: mm10
Supplementary files format and content: txt

source_name: Naïve-derived CD8+/CAR+ T cells, collected in vitro after 5 day CAR-transduction protocol

extract_protocol:
For RNAseq, cells were homogenized in QIAzol Lysis Reagent and processed using the miRNeasy Micro Kit with on-column DNase treatment, both according to manufacturer protocols. RNA purity, quantity and integrity was determined with NanoDrop and TapeStation 4200 analysis.
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used with an input of 200ng of total RNA to generate RNA-Seq libraries.

value: CAR


title: Naïve, PostCAR, Exp2, TR2


title: Naïve, PostCAR, Exp1, TR1


title: Hindlimb, E11.5, H11^B-ZRS-mCherry/SI/ZRS404G>A-eGFP-B (dual-enSERT-2), scRNA-seq

city: Irvine

first: Evgeny

last: Kvon

state: CA

address: 4310 McGaugh Hall

department: Developmental and Cell Biology

institute: University of California, Irvine

library_source: transcriptomic single cell

data_processing:
Fastq files were aligned to the mm39 genome assembly (Ensembl, GCA_000001635.9) and barcodes counted to generate a count matrix using CellRanger (10x Genomics, Cell Ranger 3.1.0). Count matrix data were analyzed using the Seurat R package, version 4.
Assembly: mm39 with custom build for mCherry and GFP
Supplementary files format and content: Tab-separated values (barcodes, features) and matrix file

source_name: Hindlimb

extract_protocol:
Hindlimb cells were dissociated with collagenase II into single cells and loaded at a concentration of 10,000 cells.
Recovery of 10,000 cells by the Chromium Next GEM Chip G Single Cell Kit 3’ Gene Expression Kit v3.1 (10X Genomics, cat no. 1000127)
Captured cells were pair-end sequenced on an Illumina NovaSeq 6000 for approximately 50,000 reads per cell.

value: FVB

tag: age

value: Hindlimb


title: EAE_BTKi_6

city: Cambridge

first: Timothy

middle: R

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

data_processing:
Quantification was performed at gene level to obtain count-level information using the Expectation-Maximization (EM) algorithm54. Differential expression. Analysis was performed using DESeq2 (version 1.30.1) in RStudio (R 4.0.2).
Assembly: Human B38 reference genome, GenCode.V24
Supplementary files format and content: Counts matrix

source_name: spinal cord

extract_protocol:
RIPA buffer + betamercaptoethanol
Bulk RNA-Seq libraries were prepared using Illumina Stranded mRNA Prep according to manufacturer’s instructions.

value: spinal cord


title: EAE_vehicle_5


title: B16-F10, Melanoma,B16-VC

city: Beijing

first: yanyan

last: zhu

state: Beijing

address: 10 Xitoutiao, Youanmen Wai, Fengtai District

institute: Chinese Institutes for Medical Research, Beijing

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10X Genomics single-cell platform. Reads were aligned to the mouse reference transcriptome mm10-2020-A
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tumor tissues were dissected from the B16F10 mouse models. Tumors were collected 14 days post injections (n=3 for each group). Tissues were digested with agitation with 2mg/ml collagenase D and 30μg/ml DNase I for 45 minutes at 37°C. Single-cell suspensions containing tumor cells were passed through 70 μm filters and stained with LIVE/DEAD Aqua (Invitrogen; Cat #L34957) for viability, as well as APC anti-mouse CD45 (Clone 30F11; BioLegend; Cat #103112).
Viable CD45+ single cells were sorted using BD FACSAriaTM III flow cytometer. Then, the cells were sent to the 10X Genomics company for library construction and sequencing.

tag: cell line

value: Melanoma

value: WT


title: EAE_BTKi_1


title: Naïve_vehicle_4


title: EAE_vehicle_6


title: EAE_BTKi_4


title: EAE_BTKi_2


title: EAE_BTKi_3


title: EAE_vehicle_4


title: Naïve_vehicle_1


title: Naïve_vehicle_2


title: EAE_BTKi_5


title: EAE_vehicle_3


title: EAE_vehicle_2


title: Naïve_vehicle_3


title: EAE_vehicle_1


title: Naïve, PostCAR, Exp2, TR1


title: RUNX2, Memory, PostCAR, Exp1, TR1


title: B16-F10, Melanoma,B16-F

description: 10X Genomics

value: FDPS-knockout (KO)


title: RUNX2, Naïve, PostCAR, Exp2, TR3


title: RUNX2, Naïve, PostCAR, Exp2, TR2


title: RUNX2, Naïve, PostCAR, Exp2, TR1


title: Naïve, PostCAR, Exp2, TR1


title: Memory, PostCAR, Exp2, TR3

source_name: Memory-derived CD8+/CAR+ T cells, collected in vitro after 5 day CAR-transduction protocol


title: RUNX2, Memory, PostCAR, Exp2, TR2


title: RUNX2, Memory, PostCAR, Exp2, TR3


title: Memory, PostCAR, Exp2, TR2


title: Memory, PostCAR, Exp2, TR1


title: RUNX2, Memory, PostCAR, Exp2, TR1


title: Naïve, PostCAR, Exp1, TR2

source_name: Naïve-derived CD8+/CAR+/GFP+ T cells, collected in vitro after 5 day CAR-transduction protocol


title: RUNX2, Memory, PostCAR, Exp1, TR1

source_name: Memory-derived CD8+/CAR+/GFP+ T cells, collected in vitro after 5 day CAR-transduction protocol


title: Memory, PostCAR, Exp1, TR2


title: Memory, PostCAR, Exp1, TR1


title: RUNX2, Naïve, PostCAR, Exp1, TR3


title: Naïve, PostCAR, Exp1, TR3


title: Naïve, PostCAR, Exp1, TR1


title: RUNX2, Naïve, PostCAR, Exp1, TR1


title: Memory, PostCAR, Exp1, TR3


title: wildtype mouse gingival tissue, non-injured control, Day 3, biol rep 3

city: Iowa City

first: Brad

last: Amendt

state: IA

address: 1-675 Bowen Science Building (BSB) - 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

data_processing:
CleanData (fastq format) - remove low quality reads and adapters [software: perl scripts in house, cutadapt]
Mapping to genome (barn format) - map the reads of each sample to the reference genome [software: HISAT2]
Transcripts assembly (gtf format) - assemble transcripts of each sample independently [software: StringTie]
Merge all assembles to creat a StringTie merged gtf [software: StringTie, gffcompare]
mRNAs expression profiling [software: StringTie]
the resulted candidate lncRNAs were further processed to remove unqualified transcripts (Length<200nt, coverage<3)
coding potential prediction - only retain five class codes (I, j, o, u, x) [software: CPC, CNCI]
differentially expresed mRNAs [software: Rpackage - edgeR]
Assembly: GRCm39, GCF_000001635.27, https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/
Supplementary files format and content: Excel (.xlsx) files include FPKM counts for each sample

source_name: gingival tissue on left jaw

growth_protocol: Mice are maintained in the animal facility of the University of Iowa. All experiments were approved by the Institutional Animal Care and Use Committee of the University of Iowa. The Irx1 knockout mouse strain (Irx1LacZNeo) was generated as previously described (PMID: 28746823).

extract_protocol:
Samples are total RNAs that were extracted from oral tissue using Qiagen miRNeasy Mini Kit. They are all collected at one time point.
For Total RNA sequencing service, RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Ribosomal RNA was removed, followed by fragmentation with divalent cation buffers in elevated temperature. The sequencing library was prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system. The following diagram depicts the workflow of library preparation for total RNA sequencing.
Total RNA Sequencing

treatment_protocol: Male and female adult mice (10-16 weeks old) were anesthetized with 2-5% isoflurane in an induction chamber connected to an evaporator. The mice were then switched to the nose cone and onto a surgical platform with heated pad. The mouth was opened with a self-retaining retractor (WPI) to ensure visual access of the lower molar rows. Puncture wounds were made using a disposable biopsy punch (0.75mm, Robbins Instruments) anterior of the first molar on the right side of the mandible to remove the gingiva (gingival epithelium and junctional epithelium included). Mice were injected with 2 mg/kg Buprenorphine (ZooPharm) for analgesia right after wounding. Mice were returned to the facility upon recovery from anesthetization and fed with regular diet (hard pellet) daily. Animals were then harvested on 3 day-post-injury (dpi) to isolate total RNA from the control and injured gingival tissue from both genotypes. All instruments were autoclaved every time before each surgery.

value: gingival tissue on left jaw

tag: injury state

value: non-injured control

tag: collection time

value: Day 3

value: wildtype


title: Irx1+/- heteozygote mouse gingival tissue, non-injured control, Day 3, biol rep 2

value: Irx1+/- heteozygotes


title: wildtype mouse gingival tissue, injured, Day 3, biol rep 2

source_name: gingival tissue on right jaw

value: gingival tissue on right jaw

value: Injured at Day 0


title: 4T1 tumor with High-Fat Diet and treated with EC359, rep2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HiSAT2 aligner (v2.1.0).
gene count measurements were obtained using FeatureCounts using refseq annotation
Assembly: mm9
Supplementary files format and content: Tab-delimited text file with columns: 1) GeneID, 2) Chr; 3) transcript start position; 4) transcript end position; 5) Strand; 6) Length of transcript; 7) read counts

source_name: 4T1 cell line

growth_protocol: For diet-induced obesity studies, Rodent diet with 60 kcal% fat was used for high-fat-diet (HFD) groups (Research Diets, Inc. #D12492) and for low-fat-diet (LFD) groups, rodent diet with 10 kcal% fat was used (Research Diets, Inc. #D12450J). After 6 weeks of diet initiation with either LFD or HFD, 5 × 10^5 4T1 cells were injected orthotopically, in a total volume of 100 μL, into the mammary fat pad of BALB/c mice. All animals continued to be fed their respective diets until euthanasia

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen, CA) and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 150bp paired-end sequencing protocol.

treatment_protocol: After tumor establishment, mice were randomized into control and treatment groups. The control group received vehicle (0.3% hydroxy propyl cellulose) and the treatment group received EC359 (LIFR Inhibitor 5 mg/kg/ip/5 days/week).

value: 4T1 cell line

value: mouse mammary carcinoma cell line

value: TNBC

tag: host mouse_strain

value: BALB/c

tag: host mouse_diet

value: high fat diet


title: Irx1+/- heteozygote mouse gingival tissue, injured, Day 3, biol rep 1


title: Irx1+/- heteozygote mouse gingival tissue, non-injured control, Day 3, biol rep 3


title: wildtype mouse gingival tissue, injured, Day 3, biol rep 3


title: Irx1+/- heteozygote mouse gingival tissue, injured, Day 3, biol rep 2


title: Irx1+/- heteozygote mouse gingival tissue, injured, Day 3, biol rep 3


title: wildtype mouse gingival tissue, non-injured control, Day 3, biol rep 1


title: RUNX2, Memory, PostCAR, Exp1, TR2

value: Splenic T cells

value: CD8+ T cell

value: Rag2-/- OT-I TCR transgenic


title: wildtype mouse gingival tissue, injured, Day 3, biol rep 1


title: Irx1+/- heteozygote mouse gingival tissue, non-injured control, Day 3, biol rep 1


title: wildtype mouse gingival tissue, non-injured control, Day 3, biol rep 2


title: 4T1 tumor with Low-Fat Diet, rep3

value: low fat diet

value: vehicle (0.3% hydroxy propyl cellulose)


title: 4T1 tumor with High-Fat Diet, rep1


title: RUNX2, Naïve, PostCAR, Exp1, TR2


title: 4T1 tumor with High-Fat Diet and treated with EC359, rep3

value: EC359 (LIFR Inhibitor 5 mg/kg/ip/5 days/week)


title: LCM74

city: San Diego

first: Young Chul

last: Kim

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

data_processing:
For quality control MultiQC version 1.8. was used. All RNASeq samples were aligned using GRCm38 reference genome using bulk RNASeq workflow in Seven Bridges using SBG Create Expression Matrix CWL1.0 workflow. Alignment and quantification were done using Salmon. Gene symbol mapping was performed using EnsDb.Mmusculus.v79.
Assembly: EnsDb.Mmusculus.v79
Supplementary files format and content: txt file with TPM of genes for each sample

source_name: Kidney

extract_protocol:
Total RNA was isolated from 70-80 microdissected SGLT2-positive tubules per sample using Arcturus PicoPure frozen RNA isolation kit and additional gDNA digestion was performed via Arcticzymes Heat & Run gDNA removal kit.
Quality and quantity of total RNA were determined by High Sensitive Tape Analysis, and cDNA library was prepared using SMARTer Stranded Total RNA-seq Kit v3-Pico Input Mammalian with 0.5 ng total RNA (DV200>30%).

treatment_protocol: Experimental mice were treated with vehicle, dapagliflozin (10mg/kg diet) or semaglutide (3nmol/kg body weight per day) for 2 weeks.

value: Kidney

tag: sample group

value: KO Akita dapa

tag: disease state

value: diabetic

value: Sglt1 KO

value: Dapagliflozin


title: LCM66


title: LCM6


title: 4T1 tumor with High-Fat Diet and treated with EC359, rep1


title: 4T1 tumor with High-Fat Diet, rep3


title: 4T1 tumor with High-Fat Diet, rep2


title: 4T1 tumor with Low-Fat Diet, rep1


title: 4T1 tumor with Low-Fat Diet, rep2


title: LCM46


title: RUNX2, Memory, PostCAR, Exp1, TR3


title: LCM78

value: WT Akita dapa

value: Sglt1 WT


title: LCM43


title: LCM88

value: WT Akita sema

value: Semaglutide


title: LCM85


title: LCM17


title: LCM99


title: LCM90


title: LCM70


title: LCM69

value: KO Akita veh

value: Vehicle


title: LCM51


title: LCM101


title: LCM7


title: LCM86


title: LCM19


title: LCM57


title: LCM4


title: LCM71


title: LCM82

value: WT Akita veh


title: LCM76


title: LCM40


title: LCM30


title: LCM8


title: LCM1


title: LCM92


title: LCM97

value: KO WT dapa

value: non-diabetic


title: LCM98


title: LCM91


title: LCM9


title: LCM65


title: LCM61


title: LCM72

value: WT WT dapa


title: LCM55


title: LCM11


title: LCM15


title: LCM94

value: KO WT veh


title: LCM10


title: LCM95


title: LCM44


title: LCM2


title: LCM87


title: LCM64


title: LCM54

value: WT WT veh


title: LCM42

value: Kidney


title: 5T33MM_20 DPI_BM

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description: 3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
Raw data scRNAseq files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: .h5 files containing raw unfiltered UMI counts in Cellranger output format and comma-delimited text files including metadata per cell

source_name: BM

extract_protocol: All methods listed in Verheye et al. A single-cell atlas of the mouse Multiple Myeloma immune microenvironment during tumor progression.

value: BM

value: 7-AAD- CD45+ 3H2-/CS1- immune cells

tag: timepoint

value: 20 DPI

tag: mouse model

value: 5T33MM Multiple Myeloma


title: 5T33MM_20 DPI_spleen

source_name: Spleen

tag: tissue

value: Spleen


title: Naive_BM

tag: cell type

value: 0 DPI

value: naïve


title: LCM67

value: Sglt1 WT


title: 5T33MM_14 DPI_BM

value: 14 DPI


title: LCM83

value: Vehicle


title: LCM58


title: pre pro B cells, Mx1-Cre Ezh2-WT, biol rep 4

city: St. Louis

first: George

middle: P.

last: Souroullas

state: Missouri

address: 660 S. Euclid Ave

department: Department of Medicine

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
reads were then aligned to the Ensembl release 76 primary assembly (GRC38/mm10) with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights7.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Assembly: GRCm38.76
Supplementary files format and content: tab-delimited text file contains CPM and RPKM values for each sample

source_name: pre pro B cells

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturer's instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Mx1-Cre mice were treated with three doses of 0.33 mg/100 ul polyinosinic-polycytidylic acid (poly I:C) injected i.p. to activate Cre expression 12 weeks before sample collection. Bone marrow was collected from all femora and tibiae of a mouse and stained with propidium iodide and these antibodies: CD19-APC, CD43-FITC, IgM-PE/Cy7, and B220-PB. Sorting was performed on a Sony iCyt Synergy BSC sorter at the Siteman Flow Cytometry Core.

value: pre pro B cells

value: Mx1-Cre, Ezh2-WT

value: poly (I:C)

tag: sorting strategy


title: LCM84

value: non-diabetic

tag: genotype


title: pre pro B cells, Mx1-Cre Ezh2-WT, biol rep 3


title: Naive_spleen


title: 5T33MM_14 DPI_spleen


title: LCM18

value: WT WT dapa

value: Dapagliflozin


title: LCM96

value: Kidney

value: KO WT dapa

value: Sglt1 KO


title: pre pro B cells, Mx1-Cre Ezh2-WT, biol rep 2


title: pre pro B cells, Mx1-Cre Ezh2-WT, biol rep 1


title: LCM75

value: WT WT veh


title: pre pro B cells, Mx1-Cre Ezh2-Y641F, biol rep 3

value: Mx1-Cre, Ezh2-Y641F


title: pro B cells, CD19-Cre Ezh2-WT, biol rep 4

source_name: pro B cells

value: pro B cells

value: CD19-Cre Ezh2-WT


title: pro B cells, CD19-Cre Ezh2-WT, biol rep 1


title: pre pro B cells, Mx1-Cre Ezh2-Y641F, biol rep 2


title: pre pro B cells, Mx1-Cre Ezh2-Y641F, biol rep 1


title: pro B cells, CD19-Cre Ezh2-Y641F, biol rep 4

value: CD19-Cre Ezh2-Y641F


title: pro B cells, CD19-Cre Ezh2-WT, biol rep 3


title: pro B cells, CD19-Cre Ezh2-WT, biol rep 2


title: pro B cells, CD19-Cre Ezh2-Y641F, biol rep 2


title: pro B cells, CD19-Cre Ezh2-Y641F, biol rep 3


title: pro B cells, Mx1-Cre Ezh2-WT, biol rep 4


title: pro B cells, Mx1-Cre Ezh2-WT, biol rep 3


title: pro B cells, Mx1-Cre Ezh2-Y641F, biol rep 2


title: pro B cells, Mx1-Cre Ezh2-WT, biol rep 2


title: pro B cells, Mx1-Cre Ezh2-Y641F, biol rep 3


city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

description:
gRNA library
Mouse 18, Sample 18-6 (Mc), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), gRNA library

library_source: other

data_processing:
In the course of the experiments, one to three libraries were generated for each sample: (1) 10x v3 Gene Expression, and (2-3) viral barcode-containing cDNA libraries (two in the case of double injection). Detailed descriptions of each sample, corresponding libraries, and FP sequences are provided in Supplementary Table X. Reads from experiments (1) and (2) were aligned to a chimeric mm39 and FP genome reference using Cell Ranger 7.0.1.
Clonal barcodes were identified using an algorithm suggested in [PMID: 35210624] with modifications available at https://github.com/serjisa/TREX.modified. Firstly, barcode sequence corrections were performed individually for each cell, enhancing robustness against artificial merging but slightly increasing clonal dropout rates.
Assembly: Chimeric mm39 with FP-CloneID contigs added
Supplementary files format and content: h5-containers, h5ad-containers and comma-separated values

molecule: other

source_name: Ectodermal and mesodermal derivatives

extract_protocol:
The embryos were removed from the uterus, sacrificed, and placed into a petri dish containing Hank’s Balanced Salt Solution (HBSS) on ice. Embryos were screened for expression of Tomato or GFP using a benchtop fluorescence stereoscope. Limbs, liver, and the ventral skin were removed. Body regions, primarily lower trunk, middle trunk, and cranial regions, were dissected separately and placed into a small Petri dish containing 2.5 mL of a cell dissociation buffer consisting of 2mg/mL Collagenase P (Roche, Sigma-Aldrich), 1X TrypLE, and 1uL/mL DNASe I, fully dissolved in HBSS (without phenol red, including Ca2+ and Mg2+). Tissue was chopped finely with a scalpel and forceps under control of stereomicroscope and transferred to 15mL falcon tubes. The tissue pieces were triturated 10X using a transfer pipette, and then 10X using a 1mL pipette. Samples were then incubated for 20 minutes at 37 C in a preheated shaking incubator set at 150 RPM, with the tubes tilted to ~60 degrees. During this time every 6-8 minutes, the samples were vortexed and triturated using a 1mL pipette. After the tissue clumps disappeared, 12.5 mL of 2% Fetal Bovine Serum (FBS) diluted in ice-cold HBSS (without phenol red, without Ca2+ and Mg2+, H6648 SIGMA) was added. The samples were centrifuged in a cold centrifuge (4C) for 15 minutes at 500 g. The supernatant was carefully removed and the pellet was resuspended in 1mL HBSS + 2% FBS and kept on ice thereafter. After centrifugation and resuspension, the cells were filtered into round-bottom polypropylene test tubes (Falcon) using a cell strainer with a 40 micrometer woven polyethylene terephthalate mesh (pluriSelect pluriStrainer SKU 43-10040-40) for downstream cell sorting.
Cells were loaded into the Chromium machine (aiming for ~10,000 cells per reaction) using the V3.1 single-cell reagent kit (10X Genomics). Following GEM creation and cell lysis, cDNA was synthesized by reverse transcription, then amplified by PCR for 12 cycles as per the manufacturer’s protocol (10X Genomics). A portion of the amplified cDNA was used to generate Gene expression libraries and then indexed using the Single Index Plate T Set A. CloneID enrichment from cDNA libraries was additionally performed based on Ratz et al 2022 to increase the retrieval of the barcodes by ~5-10%. Briefly, two nested PCR reactions were performed using Q5 error-correcting DNA polymerase to amplify the CloneID-containing region, and a third reaction was used for sample indexing using the Single Index Plate T Set A. In between each reaction, amplicons were purified by 0.8X AMPure beads using a DynaMag Magnetic separator. Indexed GE and CloneID-enrichment libraries were quantified using BioAnalyzer and/or Qubit, and then pooled prior to Illumina sequencing on a NovaSeq 6000 S2-200 v1.5 flow cell with read setup 28-8-0-166.

treatment_protocol: Injections for lentiviral gene delivery were performed according to previously published protocols. At embryonic day E7.5-E8.5, the females were anesthetized with isoflurane (4% induction, maintained at 1.5-2.5%) and placed on a heated plate for surgery. Depth of anesthesia was tested through pinching the paw. Eye gel was applied to prevent dehydration. Pain relief e.g. Buprenorphine 0.05-0.1 mg/kg was administered via subcutaneous injection 30 minutes before the first incision. All instruments were autoclaved and disinfected with chlorhexidine alcohol before surgery. The skin was disinfected with chlorhexidine alcohol, and the hair on the abdomen was removed with a shaver or hair removal agent such as Veet. A small incision was placed in the abdomen and the uterus was exposed and placed on top of gauze soaked in sterile NaCl solution, placed around the opening. The uterus was kept moist with warm NaCl solution (37C). Using a glass capillary, lentivirus (from 23-206 nL) was injected through the uterine wall into the amniotic cavity. After the embryos were injected, the uterus was brought back into the abdomen and the incisions in the muscle wall were sewn together with absorbent suture thread, and the skin was closed with suture thread or staples. The mice were taken off isoflurane and allowed to wake up in their own cage on a heating pad under supervision. Postoperative pain relief was given in the form of a subcutaneous injection of Buprenorphine (0.05-0.1 mg/kg). For embryo retrieval, the mother was euthanized via CO2 overdose and cervical dislocation, and the embryos were collected at E13.5 and euthanized via decapitation.

tag: Sex

value: Male

value: Ectodermal and mesodermal derivatives

tag: strain

tag: developmental stage


title: Mouse 18, Sample 18-6 (Mc), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), GEX

description:
Gene expression library
Mouse 18, Sample 18-6 (Mc), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), Gene expression library


description:
CloneID library
Mouse 18, Sample 18-6 (Mc), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), tdTomato amp library


description:
gRNA library
Mouse 18, Sample 18-5 (Mb), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), gRNA library


description:
CloneID library
Mouse 18, Sample 18-5 (Mb), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), tdTomato amp library


title: Mouse 18, Sample 18-4 (Ma), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), GEX

description:
Gene expression library
Mouse 18, Sample 18-4 (Ma), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), Gene expression library


description:
gRNA library
Mouse 18, Sample 18-4 (Ma), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), gRNA library


title: Mouse 18, Sample 18-3 (Lc), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), GEX

description:
Gene expression library
Mouse 18, Sample 18-3 (Lc), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), Gene expression library


title: pro B cells, CD19-Cre Ezh2-Y641F, biol rep 1

tag: treatment


description:
gRNA library
Mouse 18, Sample 18-2 (Lb), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), gRNA library


description:
gRNA library
Mouse 18, Sample 18-1 (La), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), gRNA library


description:
gRNA library
Mouse 10, Sample 10-2 (H2), Head, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


title: pro B cells, Mx1-Cre Ezh2-Y641F, biol rep 1


description:
CloneID library
Mouse 18, Sample 18-1 (La), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), tdTomato amp library


title: Mouse 10, Sample 10-2 (H2), Head, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 10, Sample 10-2 (H2), Head, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


title: Mouse 18, Sample 18-5 (Mb), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), GEX

description:
Gene expression library
Mouse 18, Sample 18-5 (Mb), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), Gene expression library


description:
gRNA library
Mouse 18, Sample 18-3 (Lc), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), gRNA library


description:
CloneID library
Mouse 18, Sample 18-4 (Ma), Upper trunk, E8.5 tdTomato-gRNA-virus (NT2), tdTomato amp library


description:
CloneID library
Mouse 18, Sample 18-3 (Lc), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), tdTomato amp library


description:
CloneID library
Mouse 18, Sample 18-2 (Lb), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), tdTomato amp library


title: Mouse 9, Sample 9-4 (F1), Head, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 9, Sample 9-4 (F1), Head, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
CloneID library
Mouse 9, Sample 9-3 (N1), Neck, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


title: Mouse 10, Sample 10-1 (T2), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 10, Sample 10-1 (T2), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


title: Mouse 9, Sample 9-3 (N1), Neck, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 9, Sample 9-3 (N1), Neck, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
gRNA library
Mouse 9, Sample 9-3 (N1), Neck, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


title: Mouse 18, Sample 18-1 (La), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), GEX

description:
Gene expression library
Mouse 18, Sample 18-1 (La), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), Gene expression library


title: Mouse 18, Sample 18-2 (Lb), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), GEX

description:
Gene expression library
Mouse 18, Sample 18-2 (Lb), Lower trunk, E8.5 tdTomato-gRNA-virus (NT2), Gene expression library


description:
CloneID library
Mouse 10, Sample 10-2 (H2), Head, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


description:
gRNA library
Mouse 9, Sample 9-2 (MT1), Middle trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


description:
gRNA library
Mouse 9, Sample 9-4 (F1), Head, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


description:
CloneID library
Mouse 9, Sample 9-4 (F1), Head, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


description:
CloneID library
Mouse 9, Sample 9-1 (LT1_CRISPR), Lower trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


description:
CloneID library
Mouse 9, Sample 9-2 (MT1), Middle trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


description:
CloneID library
Mouse 10, Sample 10-1 (T2), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


description:
gRNA library
Mouse 10, Sample 10-1 (T2), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


title: Mouse 9, Sample 9-2 (MT1), Middle trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 9, Sample 9-2 (MT1), Middle trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
gRNA library
Mouse 8, Sample 8-4 (10x108), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


description:
gRNA library
Mouse 9, Sample 9-1 (LT1_CRISPR), Lower trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


description:
CloneID library
Mouse 8, Sample 8-4 (10x108), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


title: Mouse 9, Sample 9-1 (LT1_CRISPR), Lower trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 9, Sample 9-1 (LT1_CRISPR), Lower trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
CloneID library
Mouse 8, Sample 8-2 (10x106), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


title: Mouse 8, Sample 8-3 (10x107), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 8, Sample 8-3 (10x107), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
CloneID library
Mouse 8, Sample 8-3 (10x107), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


title: Mouse 8, Sample 8-2 (10x106), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 8, Sample 8-2 (10x106), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


title: Mouse 8, Sample 8-1 (10x105), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 8, Sample 8-1 (10x105), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
CloneID library
Mouse 7, Sample 7-1 (LT2), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library

value: Wild type


description:
CloneID library
Mouse 7, Sample 7-1 (LT2), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: Mouse 7, Sample 7-1 (LT2), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 7, Sample 7-1 (LT2), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
CloneID library
Mouse 6, Sample 6-4 (F1b), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library

value: Female


title: Mouse 6, Sample 6-4 (F1b), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 6, Sample 6-4 (F1b), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
CloneID library
Mouse 6, Sample 6-3 (F1a), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 6, Sample 6-3 (F1a), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: Mouse 6, Sample 6-3 (F1a), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 6, Sample 6-3 (F1a), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


title: Mouse 8, Sample 8-4 (10x108), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), GEX

description:
Gene expression library
Mouse 8, Sample 8-4 (10x108), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), Gene expression library


description:
gRNA library
Mouse 8, Sample 8-3 (10x107), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


title: Mouse 6, Sample 6-1 (LT1), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 6, Sample 6-1 (LT1), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
gRNA library
Mouse 8, Sample 8-2 (10x106), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


title: Mouse 6, Sample 6-2 (MTN1), Middle trunk and neck, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 6, Sample 6-2 (MTN1), Middle trunk and neck, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
CloneID library
Mouse 5, Sample 5-5 (10x92), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


description:
CloneID library
Mouse 6, Sample 6-2 (MTN1), Middle trunk and neck, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


description:
CloneID library
Mouse 6, Sample 6-1 (LT1), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 5, Sample 5-5 (10x92), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 8, Sample 8-1 (10x105), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), tdTomato amp library


title: Mouse 5, Sample 5-5 (10x92), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 5, Sample 5-5 (10x92), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
gRNA library
Mouse 8, Sample 8-1 (10x105), Trunk, E7.5 tdTomato-gRNA-virus (pMR703), gRNA library


description:
CloneID library
Mouse 5, Sample 5-4 (10x91), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 5, Sample 5-4 (10x91), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: Mouse 5, Sample 5-4 (10x91), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 5, Sample 5-4 (10x91), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
CloneID library
Mouse 5, Sample 5-3 (10x90), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 5, Sample 5-3 (10x90), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: Human_Spleen, Array-seq

city: Chicago

first: Denis

last: Cipurko

state: IL

address: 900 E 57th St

department: Biological Sciences Division

institute: University of Chicago

data_processing:
Raw data processing: Fastq files from Array-seq and Visium sequencing experiments were generated using BaseSpace DRAGEN Analysis v1.3.0. To generate spatial count matrices, fastq files were processed using STARsolo from the STAR package version 2.7.10a with the mm10 mouse or CRCh38 human reference genome.  Array-seq data alignment and filtering: A custom python script was used to join STARsolo output count matrices and spot coordinates and generate a png image of points matching the x, y positions of each barcoded spot, colored based on UMI counts. The digitally generated Array-seq spot image is manually aligned with the H&E image of the same section using Illustrator. A custom python script is used to detect tissue in the H&E image and filter Array-seq data spots not under tissue.  VIsium data alignment: Visium datasets were filtered for spots under tissue and aligned to H&E images by joining the tissue positions list csv, generated by the Spaceranger v1.2.0 software to the AnnData object generated from the STARSolo count matrix.  Clustering and differential expression: For spatial gene expression analysis using Scanpy, resulting count matrices were further filtered to keep (1) genes with at least 20 UMIs across all spots, and (2) spots with more than 120 UMIs in total. For clustering, data was normalized, log10 transformed, and clustered using principal component analysis (PCA), k-nearest neighbors (k-NN) identification, and the Leiden clustering algorithm. For differential expression analysis, we used the tl.rank_genes_groups() function in Scanpy. To map tissue subregions to spatial cluster obtained with the Leiden algorithm, we used the top 15 differentially expressed genes from each cluster for manual annotation. For plotting, spatial count or cluster identity were overlaid on the greyscale H&E image using the Seaborn package.
Assembly: mm10 mouse or CRCh38 human reference genome
Supplementary files format and content: Raw count matrix data from STARSolo: Barcodes.tsv.gz, Features.tsv.gz, and matrix.mtx.gz
Supplementary files format and content: H5ad files contain raw count matricies with spot annotation of tissue subregion and scaled x,y coordinates.
Supplementary files format and content: Png files of each tissue H&E section. Spot coordinates align to pixel coordinates of corresponding H&E image files.
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

extract_protocol:
10 µm fresh-frozen, OCT-embedded tissue sections on Array-seq slides were thawed at 37°C for 1 minute and fixed for 30-45 minutes at -20°C in 100% methanol. Following fixation, slides were dried for 1 minute at room temperature, and incubated with 2 U/µL Ribolock in 5X SSC for 5 minutes at room temperature. The SSC buffer was removed from the slide surface, sections were stained for 3 minutes at room temperature with hematoxylin, washed in nuclease-free water, and stained for 1 minute at room temperature with eosin diluted 1:10 in 0.45 M Tris-Acetic acid buffer, pH = 6.0. The slide was washed in nuclease-free water and kept at room temperature until dry and imaged at 20X magnification using an Olympus VS2000 slide scanner. Tissue sections were then permeabilized with 0.1% pepsin in 0.1 M HCl at 37°C for 15-20 minutes. After permeabilization, sections were washed once with 0.1X saline-sodium citrate (SSC) buffer. Tissue sections then underwent reverse transcription, tissue removal, exonuclease I treatment. cDNAs were eluted from the array by incubating for 10 minutes at room temperature in 0.1 M KOH and neutralized by adding 0.2X volume of 1M Tris-HCl.
cDNAs were purified using a DNA Clean & Concentrator-5 kit and amplified using single-primer PCR using the KAPA HiFi HotStart ReadyMix kit. Amplified cDNAs were cleaned up using magnetic SPRISelect beads. 100 ng of amplified cDNA was tagmented using Tagment DNA TDE1 Enzyme and buffer for 5 min at 55°C and amplified by PCR using the Illumina Read1 primer and Illumina Read2-i7 reverse primers. Libraries were cleaned up using SPRISelect beads followed by gel purification using 2% E-Gel EX Agarose Gels and MinElute columns and quantified with the Qubit dsDNA High Sensitivity Assay Kit. Resulting libraries were sequenced on Illumina sequencing platforms.

value: Spleen

tag: age

value: 70 years

tag: st method

value: Array-seq


title: VP4:2_3

first: Xiaobin

last: Luo

address: Tsinghua Garden, Haidian District

institute: Tsinghua University

description:
DNBSEQ-T7 platform (PE150) with the DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.
L1EIC0602171-VP42_3

data_processing:
In terms of DNA, the aligned reads for each sample were then reconstructed using a reference-based method implemented by StringTie. To ascertain differentially expressed genes (DEGs) between two samples, transcript levels were evaluated using the transcripts per million (TPM) technique, and RSEM was employed to estimate gene abundances. Differential expression analysis was conducted using DESeq2, where DEGs demonstrating a | log2 fold change (FC) | ≥ 1 and a false discovery rate (FDR) < 0.05 (DESeq2) or FDR < 0.001 (DEGseq) were identified as significantly differentially expressed. Additionally, functional enrichment analyses such as GO and KEGG pathway assessments were conducted to determine significant enrichment of DEGs in GO terms and metabolic pathways, with a Bonferroni-corrected P-value < 0.05 against the entire transcriptome background. These analyses were performed using Goatools for GO and a Python script for KEGG pathway analysis.
Raw paired-end DNA reads were initially processed for trimming and quality control using the FAST tool with its default settings. Subsequently, the purified reads were individually mapped to the reference genome in orientation mode using HISAT2 software.
Assembly: not provided
Supplementary files format and content: raw count data of all samples have been provided on gene-exp.csv excel data

organism: Rattus norvegicus

source_name: sciatic nerve tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Qiagen) according to the manufacturer’s instructions.
RNA quality was determined using the 5300 Bioanalyser (Agilent) and quantified with the ND-2000 (NanoDrop Technologies). Only RNA samples meeting specific criteria (OD260/280 = 1.8 ~ 2.2, OD260/230 ≥ 2.0, RQN ≥ 7.0, 28S: 18S ≥ 1.0, > 1μg) were used to construct the sequencing library. RNA purification, reverse transcription, library creation, and sequencing were conducted by Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China).
The mRNA-seq transcriptome library was generated according to the Illumina® Stranded mRNA Prep, Ligation protocol (San Diego, USA) using 1 μg of total RNA. Initially, messenger RNA was isolated using the polyA selection method with oligo (dT) beads and subsequently fragmented using a fragmentation buffer. Following this, double-stranded cDNA was produced using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, USA) with random hexamer primers.
The resulting cDNA underwent end-repair, phosphorylation, and adapter ligation according to the library preparation protocol. cDNA target fragments of 300 bp were size-selected on 2% Low Range Ultra Agarose and amplified by PCR using Phusion DNA polymerase (NEB) for 15 cycles.
After post-quantification using Qubit 4.0, the sequencing libraries were sequenced on either a NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit or a DNBSEQ-T7 platform (PE150) with the DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.

value: sciatic nerve tissue


title: CC4:4-3

description:
DNBSEQ-T7 platform (PE150) with the DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.
L1EIC0602174-EXP44_3


title: Mouse 5, Sample 5-3 (10x90), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 5, Sample 5-3 (10x90), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


description:
CloneID library
Mouse 6, Sample 6-4 (F1b), Head, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: CC4:2-3

description:
DNBSEQ-T7 platform (PE150) with the DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.
L1EIC0602168-EXP42_3


description:
CloneID library
Mouse 5, Sample 5-2 (10x89), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 5, Sample 5-2 (10x89), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


description:
CloneID library
Mouse 6, Sample 6-2 (MTN1), Middle trunk and neck, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 6, Sample 6-1 (LT1), Lower trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: Control 3

description:
DNBSEQ-T7 platform (PE150) with the DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.
L1EIC0602165-CON3

value: Control


title: Mouse 5, Sample 5-2 (10x89), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 5, Sample 5-2 (10x89), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library


title: HeLa cells, XRN1 siRNA, rep 2

city: Baltimore

first: Emmanouil

last: Maragkakis

state: MD

address: 251 Bayview Blvd, 10B133 Baltimore

department: Laboratory of Genetics and Genomics (LGG)

institute: National Institute on aging

data_processing:
Basecalled using Guppy (v3.4.5)
5’ adaptors were identified and removed using Cutadapt (v2.8)
Reads were first aligned against ribosomal sequences obtained from SILVA. Non-ribosomal reads were subsequently mapped against the human genome hg38 using minimap2 (version 2.17)
Reads were also aligned against the human transcriptome.
The poly(A) tail lengths were extracted from sequenced reads using the nanopolish polya package, with quality control scores as “PASS” selectively used in our analysis.
Assembly: hg38
Supplementary files format and content: *counts_length.tab: Tab-delimited text files include transcript id based raw counts and respective average trasncript length values for each Sample
Supplementary files format and content: *polyA.tab: PolyA length
Supplementary files format and content: DESeq2 differential gene expression (Arsenite-Control)

source_name: HeLa cell line

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

extract_protocol:
Total RNA from HeLa cells was isolated using Trizol reaget (Invitrogen, Cat# 15596-018) following the manufacturer’s protocl. 75 µg of total RNA was used to isolate poly(A) mRNAs. 500-1000 ng of poly(A) mRNA was used for library preparation
RNA libraries for dRNA-Seq were prepared using direct RNA sequencing kit (Oxford Nanopore Technologies, SQK-RNA002)  following manufacturer's protocols.

treatment_protocol:
For arsenite treatment, 80-85% confluent HeLa cells were treated with 500 µM of arsenite (Sigma) whereas for combined arsenite and cycloheximide treatment, cells were treated with 500 µM of HeLa cells and 25 µg/ml of cycloheximide for 1 hour. Similarly for combined arsenite and ISRIB treatment, cells were treated with 500 µM of arsenite and 200 nM of ISRIB for 1 hour.
For siRNA treatment, HeLa cells were transfected with 20 nM of siRNA specific to XRN1 using Neon Transfection system 100 µl kit (ThermoFisher, MPK100) for 72 hours.

tag: cell line

value: HeLa cell line

value: WT

value: XRN1 siRNA

tag: time (arsenite_treatment)

value: 0 minute

tag: kit

tag: flow-cell


title: HeLa cells, XRN1 siRNA, rep 1


description:
CloneID library
Mouse 5, Sample 5-1 (10x88), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), tdTomato amp library


description:
CloneID library
Mouse 5, Sample 5-1 (10x88), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GFP amp library


title: HeLa cells, mock siRNA, rep 1

value: mock siRNA


title: HeLa cells, Arsenite, XRN1 siRNA, 60 min, rep 1

value: Arsenite, XRN1 siRNA

value: 60 minute


title: HeLa cells, Arsenite, mock siRNA, 60 min, rep 1

value: Arsenite, mock siRNA


title: HeLa cells, rep 3


description:
CloneID library
Mouse 2, Sample 2-2 (10x70), Trunk, E8.5 GFP-virus (pMR532), GFP amp library


title: Mouse 5, Sample 5-1 (10x88), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), GEX

description:
Gene expression library
Mouse 5, Sample 5-1 (10x88), Trunk, E7.5 GFP-virus (pMR532) + E8.5 tdTomato-virus (pMR671), Gene expression library

value: Male


title: Mouse 2, Sample 2-2 (10x70), Trunk, E8.5 GFP-virus (pMR532), GEX

description:
Gene expression library
Mouse 2, Sample 2-2 (10x70), Trunk, E8.5 GFP-virus (pMR532), Gene expression library

value: Ectodermal and mesodermal derivatives


title: HeLa cells, rep 1


title: Mouse 2, Sample 2-1 (10x69), Head, E8.5 GFP-virus (pMR532), GEX

description:
Gene expression library
Mouse 2, Sample 2-1 (10x69), Head, E8.5 GFP-virus (pMR532), Gene expression library

value: Wild type


title: HeLa cells, ISRIB, rep 2

value: ISRIB


title: HeLa cells, Dimethyl sulfoxide, rep 2

value: Dimethyl sulfoxide


title: HeLa cells, Cycloheximide, rep 2

value: Cycloheximide


title: HeLa cells, Dimethyl sulfoxide, rep 1


title: BAL_HTO

city: Lille

first: Jean-Claude

last: Sirard

address: 1 rue du Professeur Calmette

country: France

institute: Center for Infection and Immunity of Lille - Pasteur Institute of Lille

description: 10x Genomics

data_processing:
Cell hashing barcodes and RNA count matrices were loaded into a Seurat object.
Normalization using NormalizeData function with parameter normalization.method='CLR' has been realized on Cell hashing barcodes count matrix, followed by demultiplexing using HTODemux function with default parameters. Cells either unassigned or assigned to both barcodes were discarded.
For RNA count matrix, cells were filtered using these parameters: nFeature_RNA>100 & nCount_RNA>500 & percent.mt<30. Doublet cells were discarded based on in house function derived from DoubletFinder algorythm.
Resulting Seurat object was normalized and scaled using SCTransform with method="glmGamPoi" and variable.features.n=8000 parameters, then standard Seurat workflow was applied (RunPCA, RunUMAP, FindNeighbors and FindClusters). Most stable resolution for clustering was chosen using clustree algorythm and based on biological knowledge.
PrepSCTFindMarkers and FindAllMarkers (min.pct=0.3, only.pos=TRUE) functions were used to calculate DEGs.
Analysis has been refined selecting only neutrophil clusters to run a new UMAP.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 contains gene and hashtag by cell barcode matrix. Allcells and Neutrophils.rds contain both data and analysis for the 2 analysis performed.

source_name: Bronchoalveolar lavage

growth_protocol: Female BALB/cJRj mice (Janvier Laboratories, Saint Berthevin, France), 8 weeks old, were maintained (four by cage) in individually ventilated cages and handled in a vertical laminar flow cabinet.

extract_protocol:
Bronchoalveolar lavages were sampled using two intratracheal injections of 1 ml of PBS supplemented with 2% FCS. Cells were recovered after 5 min centrifugation at 400 g. After cell count and viability check, cell hashtag (HTO) staining (Biolegend, San Diego, CA, USA) was used following the cell-hashing protocol (TotalSeq™-A Antibodies and Cell Hashing with 10X Single Cell 3' Reagent Kit v3 3.1 Protocol).
Library was performed according to the manufacturer's instructions (single-cell 3' v3.1 protocol, 10x Genomics).

treatment_protocol: Mice were infected intranasally with 2×10^6 CFU in 30 μl PBS of Streptococcus pneumoniae serotype 1, and treated 12 hours post-infection by an intragastric administration of amoxicillin (5 μg in 200 μl sterile water) and an intranasal administration of flagellin (2.5 μg in 30 μl PBS) or PBS.

value: Bronchoalveolar lavage

value: amoxicillin +/- flagellin


title: BAL_GEX

description: 10x Genomics


title: HeLa cells, Cycloheximide, rep 1


title: 5h-nonFTO-2

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

data_processing:
First, the raw reads of m6Am-seq underwent quality control and adaptor removal using Trim_galore (version 0.6.6). Next, the clean reads were aligned to the genome (mm10, UCSC genome Browser) using HISAT2 (version 2.1.0) with default parameters. The alignment reads were then separated by strand using Samtools (version 1.9). Finally, the reads coverage was visualized using IGV (version 2.9.4) software.
Mapped reads were analyzed using the RNA methylation peak caller exomePeak with a FOLD_ENRICHMENT set to 2, and the GENE_ANNO_GTF set as RefSeq_mm10 for peak calling. To identify high-confidence peaks in the m6A-IP sample, the peak must meet the following criteria: (1) overlap between m6A-IP and m7G-IP samples, and (2) higher fold enrichment in m6A-IP (FTO (+) m6A-IP; FTO (-) m6A-IP) compared to m7G-IP. Our study only used peaks that met both criteria for m6Am signal identification criteria. An m6Am peak was identified when the peak was demethylase sensitivity between the FTO (+) and FTO (−) samples.
The m6Am peaks were identified and marked using Homer (version 4.10) with the reference genome mm10 to annotate the corresponding genes. For analyzing the sequence consensus, all m6Am peaks were taken for de novo motif analysis, using MEME (version 4.12.0), with 100 nt peak summit-centered sequences as input. The m6Am marked gene was then subjected to Gene Ontology (GO) enrichment analyses, which were carried out using Metascape and DAVID web-based tools.
Assembly: mm10
Supplementary files format and content: bw file

source_name: T cells

growth_protocol: Pcif1-floxed mice were generated by GemPharmatech using the CRISPR-cas9 system.  For later animal studies with Pcif1 KO and Pcif1 cKO mice, littermates with Pcif1flox/flox as wild-type (WT) control were used. CAG-Cre transgenic mice were obtained from GemPharmatech and Cd4-Cre transgenic mice were obtained from Cyagen Biosciences. Mice were kept in animal rooms maintained on a 12-h light- dark cycle, temperature and humidity-controlled, between 68-74 °F and 30-70%, respectively. All in vivo experiments were performed in according to the guidelines established by the Institutional Animal Care and Use Committee of the Wuhan University.

extract_protocol:
150 μg total RNA per technical replicate was isolated from naïve and activated CD8+ T cells. Size selection was first performed using a MEGAclear transcription clean- up kit (AM1908, Ambion) to deplete small RNA (< 200 nt). Purified large RNA was then fragmented to ~150 nt with magnesium RNA fragmentation buffer (E6150S, New England Biolabs) at 94 °C for 4 minutes.
10 ng of fragmented RNA were transferred into a new nuclease-free tube and used as “input”. The remaining RNA fragments were incubated with 2 μg cap-m7G antibody (RN017M, MBL) in IPP buffer (100 mM Tris- HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40, 1U/μl RNase inhibitor) for overnight at 4°C. This antibody-RNA mixture was subsequently incubated with protein A/G UltraLink Resin for 3 hours at 4°C. RNA fragments with m7G were extracted by Trizol reagent and isopropanol precipitation. 1 ng of the cap-m7G-immunoprecipitated RNA is used as “m7G-IP” and the remaining is subjected to “FTO (+)” or “FTO (-)” treatment. One-third of the “m7G-IP” RNA was used as “FTO (-)” samples. The remaining “m7G-IP” RNA was used for FTO demethylation treatment at 37 °C for 20 minutes, the demethylated RNA was purified by phenol-chloroform extraction and labeled as “FTO (+)” samples. Both the “FTO (+)” and “FTO (-)” samples were individually immunoprecipitated with the m6A antibody using the EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols. All samples, including input, m7G-IP, FTO (+), and FTO (-) RNA samples, were subjected to library construction using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634413, Takara) according to the manufacturer's protocol. Sequencing was performed on an Illumina NovaSeq 6000 with PE150.

value: T cells


title: HeLa cells, Arsenite, 60 min, rep 3

value: HeLa cell line

value: Arsenite


title: 5h-m7G-2

value: WT


title: 5h-nonFTO-1


title: HeLa cells, Arsenite, 60 min, rep 2


title: HeLa cells, Arsenite, 60 min, rep 1


title: HeLa cells, rep 2

value: Control

value: 0 minute


title: HeLa cells, Arsenite, ISRIB, 60 min, rep 2

value: Arsenite, ISRIB


title: 5h-Input-2


title: 5h-Input-1


title: HeLa cells, ISRIB, rep 1


description:
CloneID library
Mouse 2, Sample 2-1 (10x69), Head, E8.5 GFP-virus (pMR532), GFP amp library

value: Female


title: 5h-FTO-2


title: KO-A78, replicate 2, scRNAseq

city: ,Wuhan

first: Bolin

last: Xiang

address: Donghu Road, No. 115, Wuchang District

institute: Medical Research Institute and Frontier Science Center for lmmunology and Metabolism of Wuhan University

data_processing:
Sequencing was performed on the NovaSeq 6000 System (Illumina). scRNA-seq raw data were generated through 10 x platform and mapping using CellRanger (6.1.2) on the mouse reference refdata-gex-mm10-2020-A.
Assembly: mmu10(Ensembl release 100)
Supplementary files format and content: MTX fle and TSV fle contain counts for each barcodes and genes

source_name: Mouse subcutaneous tumor

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. The tumor tissue was placed in a petri dish and cut into small pieces of 2-4 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. The cells were filtered using a pre-wet 70um MACS SmartStrainer filter, and the filtrate was collected using a 50ml centrifuge tube. Rinse filter with 10ml RPMI 1640 or DMEM; Filtrate was collected with the upper centrifuge tube. Centrifuge 300 rcf at room temperature for 7 min. Carefully discard supernatant; Immediate erythrocyte lysis. Trypan blue staining was used to measure the cell activity. Add an appropriate volume of pre-cooled wash buffer, gently blow and mix until the final cell concentration is 700-1200 cells /ul.
Interrupt, end repair and add A base. Finally the SPRIselect beads was used to purify the product. Adaptor ligation and SPRIselect purification. Index PCR and SPRIselect purification. Qubit® 3.0 Flurometer Life Technologies, CA, USA ) was used to determine the library concentration. Agilent 2100 High Sensitivity DNA Assay Kit Agilent Technologies, CA, USA was used to determine the distribution of library product fragments.

value: Mouse subcutaneous tumor

value: LLC

value: Tumor cell and others


title: KO-A64, replicate 1, scRNAseq


title: HeLa cells, Arsenite, Cycloheximide, 60 min, rep 2

value: Arsenite, Cycloheximide

value: 60 minute


title: HeLa cells, Arsenite, Dimethyl sulfoxide, 60 min, rep 1

value: Arsenite, Dimethyl sulfoxide


title: 5h-FTO-1


title: HeLa cells, Arsenite, ISRIB, 60 min, rep 1


title: WT-A82, replicate 2, scRNAseq


title: p21002-s014_4x0312_wk8_PD1-ICOS_intermediate

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm of htseq-count (Anders et al., 2015)
Assembly: panTro6
Supplementary files format and content: comma delimited text file containing gene symbol, raw read counts for each sample (in columns) for each annotated transcript (in rows).

organism: Pan troglodytes

source_name: CD4+ T cell

extract_protocol:
Cells were sorted at 4C by flow cytometry into tubes containing RPMI.  Following centrifugation, cells were homogenized in 350uL Buffer RLT containing 1% 2-Mercaptoethanol and extracted using the RNeasy Micro kit (Qiagen) with on-column DNase digestion.
RNA quality was assessed using a Fragment Analyzer (Agilent), and then 0.5 nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.  Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation Kit (Illumina).  Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 20 million reads per sample.

value: CD4+ T cell

tag: population

value: PD-1/ICOS intermediate

tag: time


title: HeLa cells, Hydrogen peroxide, 120 min, rep 1

value: Hydrogen peroxide

value: 120 minute


title: HeLa cells, Arsenite, Cycloheximide, 60 min, rep 1

value: HeLa cell line


title: p21002-s012_4x0405_wk8_PD1-ICOS_negative

value: PD-1/ICOS low


title: WT-A76, replicate 1, scRNAseq


title: 4T1Opn-KO group  LYVE-1+ TAMs-7

city: Changchun

first: Lei

last: zhao

state: Jilin

address: No. 908 Mingde Street, Changchun City, Jilin Province

department: The First Hospital of Jilin University

institute: Jilin University, Changchun, China

description: 4T1Opn-KO tumor tissue

data_processing:
Quality control. The image data measured by the high-throughput sequencer are converted intosequence data (reads) by CASAVA base recognition.Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: 4T1Opn-KO tumor tissue

growth_protocol: Mammary glands of Balb/c mice were inoculated orthotopically by 5×105 4T1WT or 4T1Opn-KO cells

extract_protocol:
RNA was harvested using Rneasy mini plus (Qiagen). 1ug of total RNA was uesd for the construction of sequencing libraries
RNAlibraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Freshly excised tumor samples were placed on ice. First, the tissue samples were thoroughly washed with pre-cooled PBS on ice to remove visible blood clots. Then, the tumor samples were mechanically fragmented into small pieces using a sterile scalpel, and the mouse tumor Dissociation Kit (Miltenyi Biotec, Cat# 130-096-730), and gentleMACS Octo Dissociator with Heaters machine were used according to the manufacturer's protocols (Miltenyi Biotec, Cat#130-096-427) were further separated into single-cell suspensions. The homogenate was then filtered through a 70 μm filter (Millipore) and centrifuged at 500 × g for 10 min at 4°C. After washing with FACS buffer, cells were prepared for cell sorting.

value: 4T1Opn-KO tumor tissue

value: Macrophages


title: 4T1WT group LYVE-1+ TAMs-4

description: 4T1WT tumor tissue

source_name: 4T1WT tumor tissue

value: 4T1WT tumor tissue


title: 4T1WT group LYVE-1+ TAMs-3

description: 4T1WT tumor tissue


title: 5h-m7G-1

value: T cells

value: WT


title: p21002-s008_4x0526_wk8_PD1-ICOS_intermediate


title: 4T1 cells rIL17-2

growth_protocol: The murine 4T1 cell line was maintained in RPMI 1640 (Gibco) supplemented with 10% FBS (Gibco), 100 U/mL penicillin, and 100 U/Ml streptomycin.

treatment_protocol: 4T1 tumor cells treated with or without recombinant IL-17A cytokines.

value: epithelial


title: p21002-s010_4x0405_wk8_PD1-ICOS_high

value: PD-1/ICOS high


title: p21002-s007_4x0526_wk8_PD1-ICOS_high


title: 4T1 cells rIL17-1


title: 4T1 cells PBS-2

value: PBS


title: HeLa cells, Arsenite, Dimethyl sulfoxide, 60 min, rep 2


title: p21002-s006_4x0339_wk8_PD1-ICOS_negative


title: 4T1 cells PBS-1


title: p21002-s003_4x0395_wk11_PD1-ICOS_negative


title: p21002-s002_4x0395_wk11_PD1-ICOS_intermediate


title: p21002-s009_4x0526_wk8_PD1-ICOS_negative


title: NM_trachea

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

data_processing:
scRNA-seq reads were aligned using CellRanger (10X Genomics, version 6.0.1) with default parameters.  Initially, a CellRanger count was performed on each sample, followed by CellRanger aggregation to generate a consolidated expression matrix, a vector of genes, and a vector of barcodes.
Assembly: GRCm39 with GFP
Supplementary files format and content: CellRanger Aggregate filtered output files

source_name: trachea

extract_protocol:
5-8 month old mice were humanely euthanized and the tracheas removed. They were digested using Pronase solution (Roche) and plated on Primaria cell culture dishes for three to four hours to separate the epithelial cells from the fibroblasts. The Miltenyi Biotec Dead Cell Cleanup Kit was used to remove dead cells before passing through a 40 um filter and collection of live cells using a MiniMACS Separator column (Miltenyi Biotec). Cells were resuspended in Hams F-12 media with 10% fetal bovine serum to a final count of 1x10^6 cells/ml.
8500 cells were loaded into Chromium Next GEM Chip G (10X Genomics, #1000120) in the reverse transcription reaction according to the manufacturer’s instructions to capture at least 5000 cells.  Reverse transcription, gel beads-in-emulsion (GEM) generation, and library preparation were performed using the Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics, #1000268). Gel beads were loaded into the designated wells of the same Chip G, which was then inserted into the Chromium Controller for GEM generation.  Following GEM generation, full-length barcoded cDNAs were produced from poly-adenylated mRNA by reverse transcription, and the cDNA was amplified using twelve amplification cycles per manufacturer recommendation.  The amplified cDNA was cleaned up using SPRIselect (Beckman Coulter), and 1 µl of the cDNA was run on a bioanalyzer using the High Sensitivity DNA kit (Agilent, #5067-4627) to assess the quality and determine concentration.  To prepare Illumina sequencing-compatible cDNA libraries, the cDNA was subjected to fragmentation, followed by end repair, A-tailing, and adapter ligation.  After each of these steps, the reaction product was cleaned up using SPRIselect.  The samples were then amplified with dual sample indexes to enable multiplexing during sequencing, cleaned up, and quantified.  The cDNA was adjusted to a concentration of 0.5 ng/ml and sequenced.

value: trachea

tag: number of_tracheas


title: WT_trachea

tag: tissue

value: wild-type


title: BGH_trachea

value: bgh


title: 3T3-L1 cells, shCtrl, Day11, bio rep 4

city: Cleveland

first: Xuan

last: Xu

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

data_processing:
Remove reads containing adapters.
Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were aligned to the mouse genome (Ensembl m38.102) using TopHat version 2.1.0, SamTools version 1.3.1, and Bowtie2 version 2.2.6
Gene expression count tables were generated using HTSeq version 0.6.1
Assembly: Ensembl m38.102
Supplementary files format and content: comma-separated values text file includes normalized counts for each sample

growth_protocol: 3T3-L1 preadipocyte were maintained in DMEM supplemented with 10% FBS snd antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was collected using QIAshredder and RNeasy mini kit (Qiagen)
RNA libraries were prepared using Illumina TruSeq RNA Library Prep Kit following manufacture's protocol

treatment_protocol: Adipogenic differentiation was induced at day 0 (2 days post confluence) by adding the induction medium, which is the complete culture medium supplemented with the DMI cocktail (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, and 167 nM insulin). At day 3, the induction medium was removed and the maintenance medium (complete culture medium supplemented with 167 nM insulin) was added. At day 7, the maintenance medium was removed, and complete culture medium was added. The cells were harvested for RNA extraction at day 11.

tag: cell type

value: mature adipocyte

value: adipogenic differentiation


title: 4T1Opn-KO group  LYVE-1+ TAMs-8

description: 4T1Opn-KO tumor tissue


title: p21002-s011_4x0405_wk8_PD1-ICOS_intermediate

value: CD4+ T cell

value: PD-1/ICOS intermediate


title: HD_43

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

data_processing:
CLC Genomics Workbench 23.0.5 (Qiagen)
Adapter sequences were trimmed and sequences with less than 15 pb or without adapter nor UMI (Unique Molecular Index) were discarded
A sequential alignment strategy was used to map sequences on several databases: reference GRCh38 human genome was used, miRBase v.22.1 was considered the first annotation model, and sequences were collected as mature miRNAs
Before normalization and differential expression (DE) analysis, data were filtered, considering small RNAs with a minimum number of reads count (mean read count>2.5/group). DE analysis was performed using Generalized Linear Model (GLM) and Trimmed Mean of M-values (TMM) normalized counts (CPM) were used as input data, considering significant Benjamini-Hochberg adjusted p-values ≤ 0.05
Assembly: GRCh38 human genome
Supplementary files format and content: excel file included raw counts for each sample
Supplementary files format and content: excel file included CPM for each sample; P (IIM) vs S (HD)
Supplementary files format and content: excel file included CPM for each sample; CAM vs NCAM

extract_protocol:
Total RNA was extracted from EVs samples using the miRNeasy Serum/Plasma Advanced kit (Qiagen, Germany),
library preparation of sncRNAs from EVs samples was obtained using QIAseq® miRNA Library kit (Qiagen, Germany),

value: Peripheral blood

value: Extracellular vesicles

value: healthy donor (HD)


title: 3T3-L1 cells, shCtrl, Day11, bio rep 2


title: HD_45


title: HD_44


title: CFAP_trachea


title: HD_42


title: 3T3-L1 cells, shCtrl, Day11, bio rep 1


title: 3T3-L1 cells, shRNA #2, Day11, bio rep 2

value: Zbtb9 knockdown


title: 3T3-L1 cells, shRNA #2, Day11, bio rep 1


title: HD_41


title: 3T3-L1 cells, shRNA #1, Day11, bio rep 1


title: 3T3-L1 cells, shRNA #1, Day11, bio rep 2


title: IIM_34

value: inflammatory myopathies (IIM)


title: p21002-s001_4x0395_wk11_PD1-ICOS_high


title: CAM_12

value: CAM


title: IIM_33


title: IIM_35


title: IIM_32


title: HD_39


title: 3T3-L1 cells, shCtrl, Day7, bio rep 2

value: premature adipocyte

value: WT


title: 3T3-L1 cells, shCtrl, Day7, bio rep 3


title: 3T3-L1 cells, shCtrl, Day7, bio rep 4


title: 3T3-L1 cells, shCtrl, Day11, bio rep 3


title: 3T3-L1 cells, shCtrl, Day7, bio rep 1


title: 3T3-L1 cells, shRNA #2, Day7, bio rep 2


title: 3T3-L1 cells, shRNA #1, Day7, bio rep 2


title: HD_38


title: HD_37


title: 3T3-L1 cells, shRNA #2, Day7, bio rep 1


title: IIM_30


title: IIM_31


title: IIM_29


title: 3T3-L1 cells, shCtrl, Day3, bio rep 4


title: 3T3-L1 cells, shRNA #1, Day7, bio rep 1


title: IIM_28


title: 3T3-L1 cells, shCtrl, Day3, bio rep 3


title: IIM_27


title: HD_40


title: 3T3-L1 cells, shCtrl, Day3, bio rep 2


title: 3T3-L1 cells, shCtrl, Day3, bio rep 1


title: IIM_26


title: HD_36


title: HD_35


title: 3T3-L1 cells, shRNA #2, Day3, bio rep 2


title: 3T3-L1 cells, shRNA #2, Day3, bio rep 1


title: 3T3-L1 cells, shRNA #1, Day3, bio rep 2


title: HD_33


title: 3T3-L1 cells, shCtrl, Day0, bio rep 4

value: preadipocyte


title: HD_34


title: HD_32


title: IIM_25


title: 3T3-L1 cells, shRNA #1, Day3, bio rep 1


title: 3T3-L1 cells, shCtrl, Day0, bio rep 3


title: 3T3-L1 cells, shCtrl, Day0, bio rep 2


title: IIM_23


title: 3T3-L1 cells, shCtrl, Day0, bio rep 1


title: IIM_22


title: HD_31


title: 3T3-L1 cells, shRNA #1, Day0, bio rep 2


title: 3T3-L1 cells, shRNA #2, Day0, bio rep 1


title: 3T3-L1 cells, shRNA #1, Day0, bio rep 1


title: HD_29


title: HD_30


title: IIM_21


title: Com4

city: Hsinchu

first: Tingwen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
RSEM
Assembly: GRCm38.p6

source_name: BMDC

extract_protocol:
RNA was harvested using TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
This extracted RNA was then used to craft a sequencing library using the SureSelect XT HS2 mRNA Library Preparation Kit from Agilent.

value: BMDC

value: cGAMP nanoparticle + conditioned medium from Dox-treated 4T1 cells


title: HD_27


title: Com3


title: Com1


title: HD_28


title: IIM_24


title: IIM-20


title: CAM_11


title: GP2

value: cGAMP nanoparticle


title: IIM-19


title: Dox4

value: conditioned medium from Dox-treated 4T1 cells


title: CAM_10


title: Dox3


title: IIM_18


title: HD_26


title: GP1


title: CTL4

value: Control


title: Dox1


title: HD_25


title: CTL3


title: GP4


title: IIM_17


title: CAM_9


title: Transgenic C-IKKα mouse, 18C

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description:
Back skin cells derived from the 6-month-old C18 C-IKKα transgenic mouse
C18

data_processing:
Reads were aligned to GRCm39 mouse genome with “Rbowtie2”
counts extracted with featureCounts function from “Rsubread” and gencode annotation release 27 (gencode.vM27.annotation.gtf)
Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the normalized count values.
Assembly: GRCm39
Supplementary files format and content: normalized counts

source_name: C-IKKα sample; 6-month-old 18C (FBV) mouse skin

extract_protocol:
Total RNA from back skin derived from wild type or transgenic N-IKKα and C-IKKα  was extracted using TRIzol reagent (ThermoFisher) and purified with RNeasy MinElute Cleanup Kit (Qiagen).
cDNA library was constructed using Stranded mRNA Library Preparation Kit and sequenced in the Illumina Novaseq platform, using 150bp paired-end sequencing reads.

value: Back skin

value: C-IKK{alpha}

value: Skin cells

tag: strain background

value: FVB


title: CTL2

last: Chen


title: CAM_6

value: Peripheral blood

value: Extracellular vesicles

tag: genotype


title: CAM_8


title: Transgenic C-IKKα mouse, 16C

description:
Back skin cells derived from the 6-month-old C16 C-IKKα transgenic mouse
C16

source_name: C-IKKα sample; 6-month-old 16C (FBV) mouse skin


title: CAM_7


title: Transgenic C-IKKα mouse, 17C

description:
Back skin cells derived from the 6-month-old C17 C-IKKα transgenic mouse
C17

source_name: C-IKKα sample; 6-month-old 17C (FBV) mouse skin


title: HD_24

value: healthy donor (HD)


title: HD_23