title: monocytes from rheumatoid arthritis donor RA5, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223511

value: blood

value: primary cells

value: monocytes

value: undifferentiated M0


title: Head regenerating tip, 38hpa, repB

status: Public on Apr 28 2026

type: SRA

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description: Library name: 1984F60_38B

library_source: transcriptomic

data_processing:
Reads were aligned against the NCBI Hydra vulgaris NCBI  high contiguity assembly Hydra_vulgaris_105_v3  (GCF_022113875.1) using the STAR software (v2.7.10a). Command prototype: STAR --genomeDir INDEXDIR --sjdbGTFfile GTF --readFilesIn fqpath --outSJfilterReads Unique --outFilterType BySJout --outFilterMultimapNmax 5 --alignSJoverhangMin 8 --alignSJDBoverhangMin 4 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 50  --quantMode GeneCounts --sjdbGTFtagExonParentTranscript transcript_id --sjdbGTFtagExonParentGene gene_id --genomeChrBinNbits 12 --genomeSAsparseD 2
Genes were quantified using the STAR software (v2.7.10a) GeneCounts quantification mode (--quantMode).
Assembly: NCBI Hydra vulgaris Release Hydra_vulgaris_105_v3  (GCF_022113875.1)
Supplementary files format and content: tab-delimited file with raw (not normalized) counts for each biological sample (96 columns) and Hydra gene feature (28608 rows).

molecule: total RNA

organism: Hydra vulgaris

source_name: Whole tissue

growth_protocol: Animals are maintained in Hydra medium solution [1 mM CaCl2, 0.2 mM NaHCO3, 0.02 mM KCl, 0.02 mM MgCl2, and 0.2 mM tris-HCl (pH 7.4)] at 18°C and fed three times per week with freshly hatched Artemia nauplii.

extract_protocol:
RNA was purified using the Norgen Biotek Single Cell RNA Purification kit according to the manufacturer's protocol. RNA quality was assessed using an Agilent Bioanalyzer.
5ng of RNA was used as input to generate RNA sequencing libraries using SmartSeq2 .

treatment_protocol: We bisected Hydras and collected samples from the oral end of regenerating Hydras at one-hour intervals over a 48-hour period.

tag: tissue

value: Whole tissue

tag: strain

tag: time after_bisection

value: 38 hours


title: M1-siEHD1-3

city: Los Angeles

first: Bishuang

last: Cai

state: CA

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

country: USA

institute: University of California, Los Angeles

description:
Library name: BMDM12
bulk RNA-seq

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using the Rsubread package (featureCounts, v2.20.0) and the DESeq2 package (v1.46.0) in R (v4.4.2).
Assembly: mm10
Supplementary files format and content: comma-delimited csv files containing feature counts values

organism: Mus musculus

source_name: Bone marrow-derived macrophages

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions
RNA-seq library construction was performed at Innomics Inc. with a standard polyA-enrichment protocol.

treatment_protocol: Mouse bone marrow-derived macrophages (BMDMs) were treated with siEhd1 and incubated with lipopolysaccharide (LPS).

value: Bone marrow-derived macrophages

tag: cell type

value: BMDM

tag: Sex

value: Male

tag: age

value: 8 weeks

tag: treatment

value: BMDMs with siEhd1 and LPS treatment (M1)


title: M1-siEHD1-1

description:
Library name: BMDM10
bulk RNA-seq


title: monocytes from rheumatoid arthritis donor RA4, M2-like, LPS

city: Schlieren

first: Bojana

last: Müller-Durovic

state: Zurich

address: Wagistrasse 14

department: Department of Rheumatology

institute: University of Zurich

description: Library name: BSSE_QGF_223510

data_processing:
Base calling and demultiplexing were performed using bcl2fastq (v2.20.0.422) allowing one mismatch in index reads.
Raw sequencing reads were assessed for quality using FastQC, and summary quality metrics across samples were compiled using MultiQC.
cDNA reads were aligned to the human genome (UCSC version hg38) with STAR (v2.7.10a) using default parameters except allowing up to 10 hits in the genome (outFilterMultimapNmax 10), reporting only one alignment per multi-mapping read (outSAMmultNmax 1), and filtering reads without evidence in the splice junction table (outFilterType "BySJout").
Alignments were sorted and indexed with samtools (v1.11).
Gene-level read counts were generated using featureCounts from the Subread package (v2.0.1), counting read 5′ ends overlapping exons using the exon union model, with parameters -O, -M, --read2pos=5, --primary, -s 2, -p, -B. Gene annotation was based on Ensembl release 104.
Assembly: UCSC version hg38
Supplementary files format and content: csv file includes raw counts for each sample

organism: Homo sapiens

source_name: blood

growth_protocol: Isolation of peripheral blood mononuclear cells (PBMCs) was done by standard density-gradient centrifugation (Lymphoprep, Fresenus Kabi, Norway). Positive selection of monocytes (M0) using CD14 Microbeads (Miltenyi Biotec, Germany) was performed according to manufacturer’s instructions. Isolated monocytes were cultured in R10 media (complete medium (RPMI 1640 (Gibco) with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin- streptomycin supplemented with 2% GlutaMAX (all from GIBCO, ThermoFisher Scientific).

extract_protocol:
Cells were washed twice in ice-cold PBS and pelleted by centrifugation (4°C, 400xg, 5min). RNA extraction and on-column DNA digestion was performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Total RNA libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) from 200 ng total RNA, including poly(A) selection and strand-specific library construction.

treatment_protocol: Differentiation of CD14+ monocytes into classically and alternatively activated macrophages was achieved by supplementing the culture with 20 ng/mL LPS/IFNγ or 20 ng/mL IL-4, respectively, on a three-times-per-week basis for 8 to 11 days. For macrophage activation, a 24-hour stimulation with 100 ng/mL LPS was used.

tag: cell line

tag: disease

value: rheumatoid arthritis

tag: donor id

tag: macrophage differentiation

tag: lps treatment

value: LPS


title: monocytes from rheumatoid arthritis donor RA4, M2-like, Vehicle

description: Library name: BSSE_QGF_223509

value: Vehicle


title: control granulosa cell [CS2]

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

description:
Library name: CS2
paired-endIllumina NovaSeq 6017

data_processing:
Sequenced reads were uploaded into Partek Flow software for data analyses. We first filtered out potential rDNA and mtDNA contaminants using Bowtie 2. Next,  filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner. Raw read counts were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using the Partek EM algorithm. Raw read counts were then normalized based on the Transcripts Per Million (TPM) method, and differential expression analysis was performed by using the DESeq2(R).
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each sample

source_name: granulosa

extract_protocol:
SMART-seq v4 Ultra-low input RNA kit
The single-cell SMART-seq2 RNA-seq libraries were constructed using a modified single-cell tagged reverse transcription sequencing protocol. Briefly, mRNA from each single cell was extracted into the lysis buffer provided by the SMART-seq v4 Ultra-low input RNA kit (634891, TaKaRa, San Jose, CA, USA). mRNAs were then reversed transcribed into complementary DNA（cDNA), which was then pre-amplified and purified. Single-cell transcriptomes were subsequently tagged with unique barcodes using the Nextera XT DNA library preparation kit (FC-131-1096, Illumina, San Diego, CA, USA) and the Nextera XT Index kit v2 setA (TG-131-2001, Illumina).

value: granulosa

tag: genotype

value: WT

value: vehicle

tag: batch


title: M1-siCON-2

description:
Library name: BMDM8
bulk RNA-seq

value: BMDMs with siControl and LPS treatment (M1)


title: Head regenerating tip, 26hpa, repB

description: Library name: 1984F58_26B

value: 26 hours


title: Head regenerating tip, 26hpa, repA

description: Library name: 1984F57_26A


title: monocytes from rheumatoid arthritis donor RA4, M1-like, LPS

description: Library name: BSSE_QGF_223508

value: blood

value: primary cells

value: monocytes


title: Head regenerating tip, 38hpa, repA

description: Library name: 1984F59_38A

value: Whole tissue

value: 38 hours


title: monocytes from rheumatoid arthritis donor RA4, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223506

value: undifferentiated M0


title: M1-siCON-1

description:
Library name: BMDM7
bulk RNA-seq

value: Bone marrow-derived macrophages

value: BMDM

value: Male


title: monocytes from rheumatoid arthritis donor RA4, M1-like, Vehicle

description: Library name: BSSE_QGF_223507

value: rheumatoid arthritis


title: M0-siEHD1-2

description:
Library name: BMDM5
bulk RNA-seq

value: 8 weeks

value: BMDMs with siEhd1 (M0)


title: control granulosa cell [CS1]

description:
Library name: CS1
paired-endIllumina NovaSeq 6016

value: granulosa


title: control oocyte [CO12]

description:
Library name: CO12
paired-endIllumina NovaSeq 6011

source_name: oocyte

value: oocyte

value: WT


title: Head regenerating tip, 37hpa, repA

description: Library name: 1984F55_37A

value: 37 hours


title: control oocyte [CO14]

description:
Library name: CO14
paired-endIllumina NovaSeq 6013

value: vehicle


title: monocytes from rheumatoid arthritis donor RA4, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223505

value: blood

value: Vehicle


title: M1-siCON-3

description:
Library name: BMDM9
bulk RNA-seq

value: BMDMs with siControl and LPS treatment (M1)


title: control oocyte [CO16]

description:
Library name: CO16
paired-endIllumina NovaSeq 6015


title: control oocyte [CO15]

description:
Library name: CO15
paired-endIllumina NovaSeq 6014


title: control oocyte [CO11]

description:
Library name: CO11
paired-endIllumina NovaSeq 6010


title: monocytes from rheumatoid arthritis donor RA3, M2-like, LPS

description: Library name: BSSE_QGF_223504

value: primary cells

value: monocytes

value: LPS


title: Head regenerating tip, 25hpa, repB

description: Library name: 1984F54_25B

value: Whole tissue

value: 25 hours


title: M0-siEHD1-3

description:
Library name: BMDM6
bulk RNA-seq

value: Bone marrow-derived macrophages

value: BMDM

value: Male


title: M0-siCON-3

description:
Library name: BMDM3
bulk RNA-seq

value: 8 weeks

value: BMDMs with siControl (M0)


title: Head regenerating tip, 25hpa, repA

description: Library name: 1984F53_25A


title: Head regenerating tip, 37hpa, repB

description: Library name: 1984F56_37B


title: monocytes from rheumatoid arthritis donor RA3, M2-like, Vehicle

description: Library name: BSSE_QGF_223503

value: rheumatoid arthritis


title: M0-siCON-2

description:
Library name: BMDM2
bulk RNA-seq


title: M0-siEHD1-1

description:
Library name: BMDM4
bulk RNA-seq

value: BMDMs with siEhd1 (M0)


title: Head regenerating tip, 36hpa, repB

description: Library name: 1984F52_36B

value: 36 hours


title: monocytes from rheumatoid arthritis donor RA3, M1-like, LPS

description: Library name: BSSE_QGF_223502


title: monocytes from rheumatoid arthritis donor RA3, M1-like, Vehicle

description: Library name: BSSE_QGF_223501


title: M0-siCON-1

description:
Library name: BMDM1
bulk RNA-seq


title: control oocyte [CO9]

description:
Library name: CO9
paired-endIllumina NovaSeq 6008

value: oocyte

value: WT

value: vehicle


title: Head regenerating tip, 27hpa, repA

description: Library name: 1984F61_27A

value: 27 hours


title: control oocyte [CO8]

description:
Library name: CO8
paired-endIllumina NovaSeq 6007


title: Head regenerating tip, 36hpa, repA

description: Library name: 1984F51_36A


title: monocytes from rheumatoid arthritis donor RA3, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223500

value: blood

value: primary cells

value: undifferentiated M0


title: control oocyte [CO10]

description:
Library name: CO10
paired-endIllumina NovaSeq 6009


title: control oocyte [CO7]

description:
Library name: CO7
paired-endIllumina NovaSeq 6006


title: monocytes from rheumatoid arthritis donor RA3, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223499

value: monocytes

value: Vehicle


title: control oocyte [CO6]

description:
Library name: CO6
paired-endIllumina NovaSeq 6005


title: SIRT1intKO liver untreated biological replicate 6

city: Norwich

first: Naiara

last: Beraza

address: Rosalind Franklin Road, Norwich Research Park

country: United Kingdom

institute: Quadram Institute Biosciences

description:
Library name: 4120
Liver tissue from untreated intestinal-specific SIRT1 knockout mouse.

data_processing:
Raw sequencing reads were processed using the nf-core/rnaseq pipeline with default parameters.
Adapter trimming and quality control were performed within the nf-core/rnaseq workflow.
Reads were aligned to the reference genome using STAR.
Transcript abundance was quantified using Salmon.
Gene-level expression values were generated from the nf-core/rnaseq output for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files containing gene-level raw counts for each sample.

molecule: polyA RNA

source_name: liver

growth_protocol: Mice were maintained under standard institutional animal care conditions. Liver tissue was collected at baseline (0 h, untreated) or at 6 h and 24 h after partial hepatectomy (PHx).

extract_protocol:
Total RNA was isolated from liver tissue using QIAzol Lysis Reagent (Qiagen, 79306) according to the manufacturer’s instructions. RNA quantity and quality were assessed prior to library preparation.
Stranded mRNA libraries were prepared by Macrogen Ltd. using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following the manufacturer’s protocol. Libraries were sequenced on the Illumina NovaSeq X platform to generate 100 bp paired-end reads, with an approximate depth of 40 million paired-end reads per sample.

treatment_protocol: Mice underwent partial hepatectomy (PHx), and liver tissue was harvested at 6 h or 24 h after surgery. Untreated baseline animals (0 h) were included as controls.

value: liver

value: whole liver tissue

value: intestinal-specific SIRT1 knockout

value: untreated baseline (0 h)


title: SIRT1intKO liver untreated biological replicate 5

description:
Library name: 4119
Liver tissue from untreated intestinal-specific SIRT1 knockout mouse.


title: Head regenerating tip, 24hpa, repB

description: Library name: 1984F50_24B

value: Whole tissue

value: 24 hours


title: Head regenerating tip, 24hpa, repA

description: Library name: 1984F49_24A


title: monocytes from rheumatoid arthritis donor RA2, M2-like, LPS

description: Library name: BSSE_QGF_223498

value: rheumatoid arthritis

value: LPS


title: control oocyte [CO5]

description:
Library name: CO5
paired-endIllumina NovaSeq 6004

value: oocyte


title: SIRT1intKO liver untreated biological replicate 4

description:
Library name: 4118
Liver tissue from untreated intestinal-specific SIRT1 knockout mouse.


title: monocytes from rheumatoid arthritis donor RA2, M2-like, Vehicle

description: Library name: BSSE_QGF_223497


title: WT liver untreated biological replicate 6

description:
Library name: 4114
Liver tissue from untreated wild-type mouse.

value: WT


title: control oocyte [CO4]

description:
Library name: CO4
paired-endIllumina NovaSeq 6003

value: vehicle


title: treat-3

city: shanghai

first: xiaohui

last: chen

address: No.999, Huchenghuan Rd, Nanhui New City, Shanghai, P.R. China

country: China

institute: Shanghai Ocean University

description: Library name: sample6

data_processing:
Data Quality Control
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format (Cock P. et al, 2010), which contains sequence information and corresponding sequencing quality information.
Sequence artifacts, including reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used Fastp (version 0.23.1)(Chen S. et al, 2018) to perform basic statistics on the quality of the raw reads.
Assembly: Culter alburnus（ASM4018292v1）
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Culter alburnus

source_name: treat

extract_protocol:
Extract total RNA using the Trizol method for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo_x0002_attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.After library quality control, quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Embryos

value: Cryopreservation of  embryos


title: treat-2

description: Library name: sample5


title: SIRT1intKO liver untreated biological replicate 3

description:
Library name: 4113
Liver tissue from untreated intestinal-specific SIRT1 knockout mouse.


title: control oocyte [CO3]

description:
Library name: CO3
paired-endIllumina NovaSeq 6002


title: treat-1

description: Library name: sample4


title: monocytes from rheumatoid arthritis donor RA2, M1-like, LPS

description: Library name: BSSE_QGF_223496

value: blood

value: primary cells


title: SIRT1intKO liver untreated biological replicate 2

description:
Library name: 4112
Liver tissue from untreated intestinal-specific SIRT1 knockout mouse.


title: wt-3

description: Library name: sample3

source_name: WT

value: control


title: control oocyte [CO2]

description:
Library name: CO2
paired-endIllumina NovaSeq 6001


title: control oocyte [CO1]

description:
Library name: CO1
paired-endIllumina NovaSeq 6000


title: wt-2

description: Library name: sample2


title: monocytes from rheumatoid arthritis donor RA2, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223494

value: monocytes

value: undifferentiated M0


title: WT liver untreated biological replicate 5

description:
Library name: 4111
Liver tissue from untreated wild-type mouse.

value: liver

value: whole liver tissue


title: SIRT1intKO liver untreated biological replicate 1

description:
Library name: 4106
Liver tissue from untreated intestinal-specific SIRT1 knockout mouse.

value: intestinal-specific SIRT1 knockout

value: untreated baseline (0 h)


title: 1836_2023

city: Barcelona

first: Anna

last: Díez-Villanueva

state: Catalonia

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB

description: Library name: UDP0088

data_processing:
Adapters and low quality bases were trimmed from raw reads using trim_galore (v0.6.7) for paired end reads and default parameters.
Reads were aligned to the mouse reference genome GRCm38 using STAR (v2.7.10a) with default parameters
SAM files were converted to BAM and sorted using sambamba (v2.098.1)
The count matrix was generated with the function featureCounts of the R package Rsubread (v2.8.2) and annotation from ENSEMBL GRCm38.102
Assembly: GRCm38
Supplementary files format and content: Excel file with raw counts

growth_protocol: Animals were fed a chow diet before hepatocyte isolation through enzymatic digestion and a density gradient centrifugation. Hepatocytes were cultured overnight.

extract_protocol:
RNA was extracted using TRIzol reagent and further purified/Dnase treated with the RNeasy Mini Kit cleanup protocol (Qiagen, Hilden, Germany).
mRNA was isolated from 1.1 μg of total RNA and used to generate dual-indexed cDNA libraries with the Illumina stranded mRNA ligation kit (Illumina) and UD Indexes Set A (Illumina). Ten cycles of PCR amplification were applied to all libraries. Sequencing-ready libraries were quantified using the Qubit dsDNA HS assay (Invitrogen) and quality controlled with the Bioanalyzer 2100 DNA HS assay (Agilent). An equimolar pool was prepared with the six libraries and submitted for sequencing on a NovaSeq6000 S4 (Illumina). More than 71 Gbp were produced, with a minimum of 36.5 million of paired-end reads per sample.

value: primary hepatocytes

value: hepatocyte cell-specific Sucnr1 knockout (Hep-Sucnr1 KO)

tag: extraction day


title: monocytes from rheumatoid arthritis donor RA2, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223493

value: rheumatoid arthritis

value: Vehicle


title: wt-1

description: Library name: sample1


title: WT liver untreated biological replicate 4

description:
Library name: 4110
Liver tissue from untreated wild-type mouse.

value: WT


title: WT liver untreated biological replicate 3

description:
Library name: 4105
Liver tissue from untreated wild-type mouse.


title: 1835_2023

description: Library name: UDP0087


title: 1834_2023

description: Library name: UDP0086


title: monocytes from rheumatoid arthritis donor RA2, M1-like, Vehicle

description: Library name: BSSE_QGF_223495


title: monocytes from rheumatoid arthritis donor RA1, M2-like, LPS

description: Library name: BSSE_QGF_223492

value: LPS


title: Shg, uninfected, 70 min, biol rep 3

city: Helsinki

first: Pavlina

last: Gregorova

address: Viikinkaari 9B

country: Finland

institute: University of Helsinki

description:
Library name: Ctrl_70min_R3
R06MOC70

data_processing:
UMI were extracted by UMItools (v1.1.5).
Reads were then trimmed for polyG, adapters and quality trimmed with Cutadapt (v5.1) and fastp (v0.24.0).
Remaining reads were mapped to merged host and phage reference genomes with Bowtie2(v2.5.4).
Mapped reads were deduplicated using UMItools dedup (v1.1.5).
Read counts for each sample were called with featureCounts from subread package (v2.0.6), using custom host annotation and refseq phage genome annotation.
Assembly: NZ_CM151298.1 (host) and NC_025436.1 (phage)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: gff annotation file with merged host and phage annotion

organism: Shewanella glacialimarina

growth_protocol: Cultures grown aerobically at +15 C in 25% rMB.

extract_protocol:
Total RNA from 70 min post infection was isolated using Trizol, DNase-treated, reisolated with two rounds of acidic phenol (pH 4) and 1-bromo-3-chloropropane and precipitated with ethanol.
Total RNA was rRNA depleted using RiboCop rRNA depletion kit for G- bacteria (Lexogen) and RNA-seq libraries were prepared by Corall RNA-seq V2 with UDI 12 nt (Lexogen) according to manufacturer's protocol. Final libraries were quantified, pooled and sequenced on Illumina NovaSeq6000 to generate 50 bp pair-end reads.

treatment_protocol: Cells were infected with phage 1/4 using multiplicity of infection (MOI) 10

value: uninfected


title: 1833_2023

description: Library name: UDP0085

source_name: Flox 3

value: control Sucnr1 fl/fl


title: Shg, uninfected, 70 min, biol rep 2

description:
Library name: Ctrl_70min_R2
R05MOC70


title: monocytes from rheumatoid arthritis donor RA1, M1-like, LPS

description: Library name: BSSE_QGF_223490

value: blood


title: monocytes from rheumatoid arthritis donor RA1, M2-like, Vehicle

description: Library name: BSSE_QGF_223491

value: primary cells


title: Shg, uninfected, 70 min, biol rep 4

description:
Library name: Ctrl_70min_R4
R07MOC70


title: WT liver untreated biological replicate 1

description:
Library name: 4103
Liver tissue from untreated wild-type mouse.


title: WT liver untreated biological replicate 2

description:
Library name: 4104
Liver tissue from untreated wild-type mouse.


title: 1831_2023

description: Library name: UDP0039

source_name: Flox 1


title: monocytes from rheumatoid arthritis donor RA1, M1-like, Vehicle

description: Library name: BSSE_QGF_223489


title: Shg, uninfected, 70 min, biol rep 1

description:
Library name: Ctrl_70min_R1
R04MOC70


title: monocytes from rheumatoid arthritis donor RA1, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223488


title: 1832_2023

description: Library name: UDP0040

source_name: Flox 2


title: Shg, infected, 70 min, biol rep 4

description:
Library name: Inf_70min_R4
R07INF70

value: infected


title: WT liver 6 h post-PHx biological replicate 6

description:
Library name: 1747
Liver tissue from wild-type mouse collected 6 h after PHx.

value: 6 h after partial hepatectomy


title: Shg, infected, 70 min, biol rep 3

description:
Library name: Inf_70min_R3
R06INF70


title: monocytes from rheumatoid arthritis donor RA1, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223487

value: monocytes

value: undifferentiated M0


title: monocytes from healthy donor HD6, M2-like, LPS

description: Library name: BSSE_QGF_223486

value: healthy


title: Shg, infected, 70 min, biol rep 2

description:
Library name: Inf_70min_R2
R05INF70


title: SIRT1intKO liver 24 h post-PHx biological replicate 6

description:
Library name: 1746
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.

value: liver

value: whole liver tissue

value: intestinal-specific SIRT1 knockout

value: 24 h after partial hepatectomy


title: 16_hippo_LON5

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Library name: 28607

data_processing:
Alignment with STAR 1.4.0
Assembly: M25
Supplementary files format and content: Count matrix aligned with STAR 1.4.0 based on M25

source_name: hippocampus

extract_protocol:
For RNA analysis, brain tissues were promptly dissected on ice, flash-frozen by placing on dry ice, and stored at -80°C until further use.
RNA isolation was carried out using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA quantity and integrity were evaluated using the High Sensitivity RNA assay on the TapeStation 4200 system (Agilent). For RNA sequencing, mRNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina), with 200 ng of total RNA as the input material. The final libraries were quantified using a Qubit Fluorometer with the Qubit dsDNA HS Assay (Thermo Fisher) and the fragment size distribution was measured using the Agilent high sensitivity D1000 assay on a TapeStation 4200 system (Agilent Technologies). Sequencing was performed in paired-end mode (75 cycles) on a NovaSeq 6000 system (Illumina) using the NovaSeq S1 v1.5 (200 Cycles) chemistry. Raw sequencing data were demultiplexed using bcl2fastq2 v2.20.

treatment_protocol: Eight weeks-old male C57Bl/6J wild-type mice were randomized for the different treatment groups by an independent investigator. α-IgLON5 AABs and non-reactive human monoclonal IgG (mCtrl),  and PBS as controls - were delivered continuously into the right lateral ventricle over the course of 14 days, with a flow rate of 0.25 μl/h. Antibody cerebroventricular infusion was performed unilaterally using osmotic pumps (model 1002, Alzet, Cupertino, CA), which were loaded 24 h prior to surgical implantation. For pump implantation, mice were placed in a stereotaxic frame and a cannula was inserted into the right ventricle (Coordinates: 0.2 mm posterior and ± 1.00 mm lateral from bregma, depth 2.2 mm).

value: hippocampus

value: C57Bl/6J wild-type mice

value: neurons


title: 17_hippo_LON5

description: Library name: 28608


title: Shg, infected, 70 min, biol rep 1

description:
Library name: Inf_70min_R1
R04INF70

value: WT


title: 9_hippo_LON5

description: Library name: 28606


title: SIRT1intKO liver 24 h post-PHx biological replicate 7

description:
Library name: 1748
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.


title: monocytes from healthy donor HD6, M2-like, Vehicle

description: Library name: BSSE_QGF_223485

value: Vehicle


title: WT liver 24 h post-PHx biological replicate 4

description:
Library name: 1743
Liver tissue from wild-type mouse collected 24 h after PHx.


title: SIRT1intKO liver 24 h post-PHx biological replicate 5

description:
Library name: 1742
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.


title: 8_hippo_LON5

description: Library name: 28605


title: 75_hippo_IgG

description: Library name: 28604

value: mIgG


title: 8988T, KRAS KO, Day32

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: Library name: KOD32

library_source: genomic

data_processing:
Conversion of BAM to fastq with samtools (v1.3)
Mageck (v0.5.9.5) count function to generate read counts for each sample
Assembly: hg19
Supplementary files format and content: .txt file containing read counts in a table format
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: pancreas

growth_protocol: Growth was in DMEM with 10% FBS, maintaining 500x representation, grown for 4 days, 8 days, or 14 population doublings as designated.

extract_protocol:
Genomic DNA (gDNA) was isolated using Maxi (3 × 10 7 –1 × 10 8 cells), Midi (5 × 10 6 –3 × 10 7 cells), and Mini (<5 × 10 6 cells) kits according to the manufacturer's protocol (Qiagen).
PCR of gDNA and pDNA was performed to attach sequencing adaptors and barcode samples, which were divided into multiple 100 μl reactions (total volume) containing a maximum of 10 μg gDNA. Per 96-well plate, a master mix consisted of 75 μl ExTaq DNA Polymerase (Clontech), 1,000 μl of 10× Ex Taq buffer, 800 μl of dNTP provided with the enzyme, 50 μl of P5 stagger primer mix (stock at 100 μM concentration), and 2,075 μl water. Each well consisted of 50 μl gDNA plus water, 40 μl PCR master mix, and 10 μl of a uniquely barcoded P7 primer (stock at 5 μM concentration). PCR cycling conditions: an initial 1 min at 95 °C; followed by 30 s at 94 °C, 30 s at 52.5 °C, 30 s at 72 °C, for 28 cycles; and a final10 min extension at 72 °C. P5/P7 primers were synthesized at Integrated DNA Technologies (IDT). Samples were purified with Agencourt AMPure XP SPRI beads according to manufacturer's instructions (Beckman Coulter, A63880).

treatment_protocol: Treatment was Brunello library at MOI of 1 and selection with puromycin for 7 days

value: pancreas

value: PDAC

value: KRASnull

tag: time


title: monocytes from healthy donor HD6, M1-like, Vehicle

description: Library name: BSSE_QGF_223483

value: blood

value: primary cells


title: 8988T, KRAS KO, Day22

description: Library name: KOD22


title: monocytes from healthy donor HD6, M1-like, LPS

description: Library name: BSSE_QGF_223484

value: monocytes

value: LPS


title: WT liver 24 h post-PHx biological replicate 3

description:
Library name: 1740
Liver tissue from wild-type mouse collected 24 h after PHx.

value: liver


title: 37_hippo_IgG

description: Library name: 28603


title: WT liver 24 h post-PHx biological replicate 2

description:
Library name: 1739
Liver tissue from wild-type mouse collected 24 h after PHx.

value: whole liver tissue


title: 8988T, KRAS KO, Day8

description: Library name: KOD8


title: 15_hippo_IgG

description: Library name: 28602


title: 8988T, KRAS KO, Day4

description: Library name: KOD4


title: WT liver 6 h post-PHx biological replicate 5

description:
Library name: 1738
Liver tissue from wild-type mouse collected 6 h after PHx.

value: 6 h after partial hepatectomy


title: WT liver 6 h post-PHx biological replicate 4

description:
Library name: 1737
Liver tissue from wild-type mouse collected 6 h after PHx.


title: 8988T, KRAS intact, Day22

description: Library name: IntactD22

value: KRAS G12V/ KRAS WT


title: monocytes from healthy donor HD6, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223482

value: healthy

value: undifferentiated M0


title: WT liver 6 h post-PHx biological replicate 3

description:
Library name: 1736
Liver tissue from wild-type mouse collected 6 h after PHx.


title: 8988T, KRAS intact, Day8

description: Library name: IntactD8


title: 74_hippo_PBS

description: Library name: 28599

value: hippocampus

value: C57Bl/6J wild-type mice

value: neurons

value: PBS


title: monocytes from healthy donor HD5, M2-like, Vehicle

description: Library name: BSSE_QGF_223479

value: Vehicle


title: SIRT1intKO liver 6 h post-PHx biological replicate 5

description:
Library name: 1735
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 6 h after PHx.

value: intestinal-specific SIRT1 knockout


title: 38_hippo_PBS

description: Library name: 28598


title: WT liver 6 h post-PHx biological replicate 2

description:
Library name: 1734
Liver tissue from wild-type mouse collected 6 h after PHx.

value: WT


title: 33_hippo_PBS

description: Library name: 28597


title: monocytes from healthy donor HD5, M2-like, LPS

description: Library name: BSSE_QGF_223480

value: blood


title: L4a1 RNA rep3

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

description: Library name: L4a1 RNA rep3

data_processing:
Each sample R1 and R3 reads (containing the barcode) were mapped with bowtie2 (--very-sensitive) to the barcode-oligo association list We applied several quality filters on the resulting alignments. We first filtered out read pairs that didn’t map as proper pairs, and then ensured the mapped sequence completely matched the known barcode sequence by requiring that both R1 and R3 reads have CIGAR stings = 15M, MD flags = 15 and a mapping quality of at least 20. We consolidated read abundance per barcode by selecting only reads with unique UMIs, the result being abundance counts for each barcode, across each replicate library of each cell type for both RNA and DNA.
Assembly: GRCh37
Supplementary files format and content: oligos_to_barcodes.txt file contains pairs of oligo-barcode associations. activity_and_differential_activity.txt file contains for each oligo the RNA read count, DNA read count, activity (classification, estimate and FDR), and differential activity for each pair of alleles (logFC and FDR).

source_name: Fetal chondrocytes

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen).
For DNA/RNA barcode sequencing, mRNA was treated with Turbo DNase to remove contaminating DNA, and reverse transcribed with SuperScript IV (Invitrogen) using a primer containing unique molecular identifiers (UMIs). Resulting cDNA and genomic DNA was split into multiple reactions to reduce PCR jack-potting effects and barcode amplification performed with NEBNext high-fidelity polymerase for three cycles using a forward primer containing P5 adaptor and a sample index and a reverse primer containing P7 adaptor and UMIs. PCR products were purified with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification using P5 and P7 primers. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA-barcode association, CRE-barcode fragment is amplified with a forward primer upstream from CRE and a reverse primer downstream from barcode, using a plasmid library as a template, followed by AMPure XP beads purification and sequencing.

value: Fetal chondrocytes


title: 10_hippo_IgG

description: Library name: 28600

value: mIgG


title: monocytes from healthy donor HD5, M1-like, LPS

description: Library name: BSSE_QGF_223478

value: primary cells

value: monocytes

value: LPS


title: monocytes from healthy donor HD5, M1-like, Vehicle

description: Library name: BSSE_QGF_223477


title: monocytes from healthy donor HD5, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223476


title: L4a1 DNA rep3

description: Library name: L4a1 DNA rep3


title: 32_hippo_PBS

description: Library name: 28596


title: SIRT1intKO liver 6 h post-PHx biological replicate 4

description:
Library name: 1733
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 6 h after PHx.

value: liver

value: whole liver tissue

value: 6 h after partial hepatectomy


title: monocytes from healthy donor HD6, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223481

value: healthy

value: undifferentiated M0


title: 8988T, KRAS intact, Day4

description: Library name: IntactD4

value: pancreas

value: PDAC

value: KRAS G12V/ KRAS WT


title: L4a1 RNA rep2

description: Library name: L4a1 RNA rep2


title: WT liver 6 h post-PHx biological replicate 1

description:
Library name: 1732
Liver tissue from wild-type mouse collected 6 h after PHx.


title: monocytes from healthy donor HD4, M2-like, LPS

description: Library name: BSSE_QGF_223474


title: 17_crtx_LON5

description: Library name: 28594

source_name: cortex

value: cortex

value: C57Bl/6J wild-type mice

value: neurons


title: SIRT1intKO liver 6 h post-PHx biological replicate 3

description:
Library name: 1731
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 6 h after PHx.

value: intestinal-specific SIRT1 knockout


title: 14_hippo_PBS

description: Library name: 28595

value: hippocampus

value: PBS


title: 16_crtx_LON5

description: Library name: 28593


title: L4a1 RNA rep1

description: Library name: L4a1 RNA rep1

value: Fetal chondrocytes


title: monocytes from healthy donor HD5, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223475

value: blood

value: primary cells

value: monocytes

value: Vehicle


title: SIRT1intKO liver 6 h post-PHx biological replicate 2

description:
Library name: 1730
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 6 h after PHx.

value: liver

value: whole liver tissue

value: 6 h after partial hepatectomy


title: monocytes from healthy donor HD4, M1-like, LPS

description: Library name: BSSE_QGF_223472

value: healthy

value: LPS


title: 9_crtx_LON5

description: Library name: 28592


title: SIRT1intKO liver 6 h post-PHx biological replicate 1

description:
Library name: 1729
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 6 h after PHx.


title: L4a1 DNA rep1

description: Library name: L4a1 DNA rep1


title: L4a1 DNA rep2

description: Library name: L4a1 DNA rep2


title: monocytes from healthy donor HD4, M2-like, Vehicle

description: Library name: BSSE_QGF_223473


title: SIRT1intKO liver 24 h post-PHx biological replicate 4

description:
Library name: 1725
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.

value: 24 h after partial hepatectomy


title: 75_crtx_IgG

description: Library name: 28590

value: cortex

value: mIgG


title: L3a3 DNA rep3

description: Library name: L3a3 DNA rep3


title: monocytes from healthy donor HD4, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223469

value: undifferentiated M0


title: 37_crtx_IgG

description: Library name: 28589

value: C57Bl/6J wild-type mice

value: neurons


title: WT liver 24 h post-PHx biological replicate 1

description:
Library name: 1727
Liver tissue from wild-type mouse collected 24 h after PHx.

value: WT


title: L3a3 DNA rep2

description: Library name: L3a3 DNA rep2

value: Fetal chondrocytes


title: monocytes from healthy donor HD4, M1-like, Vehicle

description: Library name: BSSE_QGF_223471

value: blood


title: 8_crtx_LON5

description: Library name: 28591


title: monocytes from healthy donor HD3, M2-like, LPS

description: Library name: BSSE_QGF_223468

value: primary cells


title: L3a3 RNA rep3

description: Library name: L3a3 RNA rep3


title: 11_crtx_IgG

description: Library name: 28587


title: 10_crtx_IgG

description: Library name: 28586


title: e15.5_2_slide_seq

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

description:
Library name: e15.5_2_slide_seq
e15.5_2_slide_seq

library_source: transcriptomic single cell

data_processing:
We acquired the unfiltered feature-barcode matrix for each sample by using Space Ranger (v2. 1. 0) ‘count’ command with manually selected dots and reorient-images enabled) on the demultiplexed FASTQ files and associated image, along with the prebuilt mm10 genome reference 2020-A. After it detected tissue, aligned reads, generated feature-spot matrices, and positioned spots, we then used Seurat for all further analyses. In each slide, Seurat objects were created by Load10X_Spatial function and then normalized with natural-log transformation using log1p. Similarly, we obtained the unfiltered matrix of curioseq data by using Curio seeker (v2.0) with custom GRCm38 genome reference (add eGFP). Specifically, Curio seeker was first used to extract bead and molecular barcodes for the raw FASTQ files of each sample and filter beads obtained from sequencing data against the bead barcode whitelist. After filtering out beads with Hamming distance greater than 2 and creating new seurat object, we manually normalized counts with natural log.
We splitted out the Visium image which has more than one tissue. This process can facilitate the integration with scRNA-seq dataset in later section. We cut segments based on exact positions. After subsetting, we can visualize the certain stage cells either on the full image, or a cropped image. (Stage E11.5, P0, E14.5, E16.5 have two tissues in one image, E17_E11 and P2_E14 from second experiment have three tissues in same image.) In Curio seq samples, we first set filter range of each coordinate and then store the shrank image in a new Seurat object.
Assembly: GRCm38
Supplementary files format and content: rds

source_name: heart

extract_protocol:
Mouse hearts from CD1 wildtype, Wt1-CreER-mTmG, and Wt1-CreER-DTA mice were harvested and directly embeded in OCT. Then the hearts were sectioned and used for Visium or Slide-seq profiling.
The heart sections were processed by following the protocol for 10X Genomics Visium Spatial gene expression kit (1000187); For the Slide-seq experiments, we followed the updated protocol in 2023 October from Curio-Bio company.

value: heart

value: cardiac cells

value: CD1 wildtype


title: monocytes from healthy donor HD3, M1-like, LPS

description: Library name: BSSE_QGF_223466

value: monocytes


title: 74_crtx_PBS

description: Library name: 28585

value: PBS


title: L3a3 DNA rep1

description: Library name: L3a3 DNA rep1


title: monocytes from healthy donor HD4, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223470

value: healthy


title: e10.5_slide_seq

description:
Library name: e10.5_slide_seq
e10.5_slide_seq;


title: L3a2 DNA rep3

description: Library name: L3a2 DNA rep3


title: Ascitic fluid cells from ovarian cancer mouse. PEP37 immunized_1

city: Mexico city

first: José

middle: Jesús

last: Guzmán-Mendoza

address: Av. Instituto Politecnico Nacional 2508,

department: Infectómica y Patogénesis Molecular

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados

description: Library name: PEP37_1

data_processing:
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage. Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million)
In groups with different conditions, genes or transcripts that express  differentially are filtered out through statistical hypothesis testing.
Assembly: mm10
Supplementary files format and content: xlsx file include Read Count, FPKM and TPM for each sample

source_name: Ascitic fluid

growth_protocol: ID8-Defb29/Vegf-a cell line was cultured in high-glucose DMEM (Sigma‒Aldrich) supplemented with 5% FBS (Corning) and 1% insulin, transferrin, and sodium selenite (ITS) (Sigma‒Aldrich) at 37 °C in 5% CO₂. The cells were used within 10 passages to maintain quality.

extract_protocol:
Total RNA from ascites-derived cells from each immunized mouse was extracted via an RNeasy Mini Kit (Cat. 74104, Qiagen). Following the provider's protocol, the DNA was further cleaned with a DNasa I amplification grade Kit (Cat. 18068015, Invitrogen).
RNA libraries were prepared using TruSeq stranded mRNA via the NovaSeqX platform and RNA sequencing

treatment_protocol: Mice were immunized with 10 µg of each antigen (f-CNTs or PEP37)

value: Ascitic fluid

value: Peritoneal cells and ID8-Defb29/Vegf-a

value: Perinoteal cells

value: PEP37 immunization

value: Ovarian cancer model ID8-Defb29/Vegf-a innoculated i.p via

value: Female

value: 6 weeks after  ID8-Defb29/Vegf-a innoculation


title: SIRT1intKO liver 24 h post-PHx biological replicate 3

description:
Library name: 1724
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.

value: liver

value: whole liver tissue

value: intestinal-specific SIRT1 knockout

value: 24 h after partial hepatectomy


title: 38_crtx_PBS

description: Library name: 28584

value: cortex

value: C57Bl/6J wild-type mice

value: neurons


title: L3a3 RNA rep2

description: Library name: L3a3 RNA rep2

value: Fetal chondrocytes


title: L3a2 RNA rep2

description: Library name: L3a2 RNA rep2


title: SIRT1intKO liver 24 h post-PHx biological replicate 2

description:
Library name: 1722
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.


title: Colon, D10, Stroma fraction, gene expression

city: Stockholm

first: Jennifer

last: Fransson

address: Karolinska Institutet

country: Sweden

institute: Karolinska Institutet

data_processing:
Reads were analyzed using CellRanger v 6.0.2 (10X Genomics). The first run did not capture the feature barcodes of some samples due to a mistake, for which reason .tsv-files containing the feature barcode counts for those samples.
Gene expression matrices were analyzed using the Seurat 4.1.1 pipeline
Assembly: mm10
Supplementary files format and content: .h5-files for each sample and .tsv-files with feature barcode counts for some samples.

source_name: colon

extract_protocol:
Colonic cells were isolated as previously described with minor alterations (Villablanca et al., 2011). Briefly, colonic tissue was cleaned from fat, opened longitudinally and cut into 1 cm pieces. Tissues from mice from the same treatment group and time point were pooled. Tissues were incubated for 30 min at 37 °C in 20 ml HBSS with 5% FCS, 5 mM EDTA, 1 mM DTT and 15 mM HEPES while shaking gently. The epithelium-enriched supernatant was then filtered through a 100 µm strainer, washed in PBS with 5% FCS and 1 mM EDTA, and cells were recovered at the interface of a 44-67% Percoll gradient. The remaining tissue was washed twice in PBS and digested in 10 ml of serum-free HBSS with Liberase TL (0.15 mg/ml, Roche) and 0.1 mg/ml DNase I (Roche) at 37 °C at 600 rpm for 60 min. After filtration through a 100 μm cell strainer, lamina propria-enriched cells were washed with PBS with 5% FCS and 1 mM EDTA and separated on a 44-67% Percoll gradient. Both epithelium-enriched and lamina propria-enriched fractions were stained with TER-119 Pacific Blue, CD45.2 PE/Cyanine7 and EpCAM FITC surface antibodies (BioLegend) for cell type assignment. Cells from the lamina propria were additionally labeled with TotalSeq antibodies (BioLegend) targeting CD90.2, CD3, CD4, KLRG1, CD127, Ly-6C, CD64, CD11b, CD11c, CD103 and Ly-6G according to manufacturer’s instructions. After additional staining with DAPI for live/dead cell identification, cells were sorted using Sony SH800 Cell Sorter into 15mL tubes filled with complete RPMI medium with 10% FCS. Epithelial cells were sorted from the epithelium-enriched fraction by gating EpCAM+/CD45- cells. Immune and stromal cells were sorted from the lamina propria-enriched fraction, by gating EpCAM-/CD45+ and EpCAM-/CD45- cells, respectively. Approximately 16000 cells per sample were loaded onto the 10X Genomics Chromium Controller and processed with the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics).
Libraries were constructed following the manufacturer’s guidelines (Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics)), with TotalSeq-derived barcodes being retained only for the immune cell fractions.
Sequencing was performed by Novogene Co. Ltd (UK) (Rag2-/- samples) or NGI Sweden (SCID samples) on NovaSeq 6000 sequencers with a targeted sequencing depth of 300M reads per gene expression sample and 50M reads per TotalSeq-derived sample. Read length was PE150 (Novogene) or 28-10-10-150 for gene expression samples and 28-10-10-25 (NGI) for TotalSeq-derived samples.

value: colon

value: Stroma

value: Rag2 KO

value: CD45RBhi transfer

value: no


title: 15_crtx_IgG

description: Library name: 28588

value: mIgG


title: monocytes from healthy donor HD3, M2-like, Vehicle

description: Library name: BSSE_QGF_223467

value: blood

value: primary cells

value: monocytes

value: healthy

value: Vehicle


title: L3a3 RNA rep1

description: Library name: L3a3 RNA rep1


title: e15.5_1_slide_seq

description:
Library name: e15.5_1_slide_seq
e15.5_1_slide_seq

value: heart

value: cardiac cells

value: CD1 wildtype


title: L3a2 RNA rep3

description: Library name: L3a2 RNA rep3


title: monocytes from healthy donor HD3, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223463

value: undifferentiated M0


title: 32_crtx_PBS

description: Library name: 28582

value: cortex

value: C57Bl/6J wild-type mice

value: neurons

value: PBS


title: monocytes from healthy donor HD3, M1-like, Vehicle

description: Library name: BSSE_QGF_223465


title: SIRT1intKO liver 24 h post-PHx biological replicate 1

description:
Library name: 1721
Liver tissue from intestinal-specific SIRT1 knockout mouse collected 24 h after PHx.

value: liver

value: whole liver tissue

value: intestinal-specific SIRT1 knockout

value: 24 h after partial hepatectomy


title: 14_crtx_PBS

description: Library name: 28581


title: monocytes from healthy donor HD2, M1-like, Vehicle

description: Library name: BSSE_QGF_223459

value: blood


title: L3a1 RNA rep3

description: Library name: L3a1 RNA rep3

value: Fetal chondrocytes


title: Bcat_GOF_day5

city: Piscataway

first: Michael

last: Verzi

address: 145 Bevier Road,

department: Department of Genetics

description:
Library name: Sample 4
10X Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Matrices from single-cell counts were processed and analyzed through Scanpy(v1.8.2) and custom Python scripts on Google Colab.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Stromal cells

extract_protocol:
Briefly, freshly harvested intestine was flushed with cold PBS, cut into 2 cm open fragments, followed by two incubation steps under constant rotation with pre-digestion buffer (HBSS containing 10% FBS, 10 mM HEPES and 5 mM EDTA) at 37°C for 20 minutes twice. Next, tissues were rinsed with wash buffer (HBSS containing 2% FBS, 10 mM HEPES), and  incubated with pre-warmed digestion buffer (RPMI medium containing 10% FBS, 1% P/S, 15 mM HEPES, 25 U/mL of collagenase IV (Worthington LS004186), 100 U/mL of DNase I (Sigma D4513), 0.3 g/100 mL of Dispase II (Gibco 17105041)) and rotated at 37°C for 30 minutes. Suspension of digested tissue was vortexed vigorously for 20 seconds every 10 minutes to release single cells. Cell solution was passed through a 40 μm cell strainer and cells were pelleted by centrifugation at 400 g for 5 minutes at 4 °C and resuspended in RPMI medium containing 10% FBS.
Library construction was performed per manufacturer's protocol using 10X Genomics Chromium Next GEM Single Cell 5' Kit V2

value: Stromal cells

value: Mesenchyme


title: monocytes from healthy donor HD2, M1-like, LPS

description: Library name: BSSE_QGF_223460

source_name: blood

value: primary cells

value: monocytes

value: healthy

value: LPS


title: Ascitic fluid cells from ovarian cancer mouse. Non-immunized control_1

description: Library name: CAOV-NT_1

value: Ascitic fluid

value: Peritoneal cells and ID8-Defb29/Vegf-a

value: Perinoteal cells

value: WT

value: No treatment

value: Ovarian cancer model ID8-Defb29/Vegf-a innoculated i.p via

value: Female

value: 6 weeks after  ID8-Defb29/Vegf-a innoculation


title: L3a2 DNA rep2

description: Library name: L3a2 DNA rep2


title: monocytes from healthy donor HD2, M2-like, Vehicle

description: Library name: BSSE_QGF_223461

value: Vehicle


title: Ascitic fluid cells from ovarian cancer mouse. F-CNTs immunized_1

description: Library name: F-CNTs_1

value: f-CNTs immunization


title: control oocyte [CO13]

description:
Library name: CO13
paired-endIllumina NovaSeq 6012

value: oocyte

value: vehicle


title: 33_crtx_PBS

description: Library name: 28583

value: cortex

value: C57Bl/6J wild-type mice

value: neurons

value: PBS


title: Bcat_GOF_day4

description:
Library name: Sample 3
10X Genomics

value: Stromal cells

value: Mesenchyme


title: Control, sample 3, HTO

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description: Library name: Sample3_HTO

library_source: other

data_processing:
The mRNA (GEX) data was mapped to the UCSC mm10 genome reference using STARsolo (STAR version 2.7.10a) (Dobin et al. 2013). Gene quantification made use of a custom GFT file based on the ensembl gene annotation (version 102) and was filtered to only include transcripts of biotypes "protein_coding", "lncRNA" and all B- and T-cell receptor gene transcripts. The cell barcode whitelist used for STAR is the file 3M-february-2018.txt provided by 10x. Other non-standard command line options for STAR include "--outFilterType BySJout --outFilterMultimapNmax 10 --outSAMmultNmax 1 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Forward --outFilterScoreMin 30 –soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 –soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloMultiMappers EM --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB".
The cell hashtag (HTO) data was also mapped and quantified with STAR, by using the same cell barcode whitelist and merging of GEX and HTO datasets made use of the corresponding feature barcode translation table from 10x. The genome index was buil from the HTO sequences as well as the GTF file used for quantification. Additional command line options included "--outSAMtype BAM SortedByCoordinate –outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Forward --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 –soloFeatures Gene".
Assembly: mm10
Supplementary files format and content: Three files per sample and library type (GEX/HTO) which are the raw output of STARsolo: 1. gene counts (<sample_id>_<lib_type>_matrix.mtx), 2. tab separated text file with gene/HTO IDs (<sample_id>_<lib_type>_features.tsv), 3. tab separated text file with cell barcodes (<sample_id>_<lib_type>_barcodes.tsv)
Library strategy: CITE-seq

molecule: other

extract_protocol:
The colon was isolated from the mouse, opened longitudinally, and cleaned with PBS to remove feces and debris from the lumen. The intestinal epithelium was isolated by incubation in PBS/5 mM EDTA and shaking for 10 min at 37˚C , repeated at least two times, and supernatants were collected and pelleted. After the epithelium was removed, the colon was twice washed, vortexed, and then incubated in PBS/EDTA for 10 min. The colon was then cut as small as possible and digested with RPMI 1640 containing 0.5 mg/ml Collagenase VIII (Sigma-Aldrich #C2139) and 10 U/ml DNase I (Roche #4536282001) for 15 min at 37 ˚C in a water bath with 200 rpm shaking and vortexed every 5 min. Supernatants were collected and passed through a 70-μm cell strainer, and the cells were pelleted by centrifuging at 600 x g for 5 min at 4 ˚C to receive the lamina propria cells. After counting the cells, they were further processed for further treatment, hashtag antibodies labeled-colonic lamina propria monocytes and macrophages were isolated and stained for CCR2, Ly6c, MHC II, CD11b, and CD64. After gating on CD11b+cells, the mononuclear cells were distinguished into CCR2+ or CD64+ mononuclear cells
Hashtag antibodies labeled-cell suspension volumes aiming at a targeted recovery of 20,000 cells were loaded into wells of a single 10x Genomics Chromium Single Cell Controller (one well per two biological replicates). Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 were used according to the manufacturer’s instructions for single-cell capture, cDNA, and library preparation. Single-cell libraries were then sequenced on one flow-cell of an Illumina NovaSeq 6000 sequencer machine at the Genomics Facility Basel of the ETH Zurich (with 91nt-long R2 reads).

value: colon

value: CD64+CCR2+ macrophages/monocytes

value: CT


title: monocytes from healthy donor HD2, M2-like, LPS

description: Library name: BSSE_QGF_223462

value: blood

value: primary cells

value: monocytes

value: healthy

value: LPS


title: Control 2

description:
Library name: Sample 5
10X Genomics


title: monocytes from healthy donor HD3, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223464

value: undifferentiated M0


title: L3a2 RNA rep1

description: Library name: L3a2 RNA rep1

value: Fetal chondrocytes


title: Control, sample 4, HTO

description: Library name: Sample4_HTO


title: L3a1 DNA rep3

description: Library name: L3a1 DNA rep3


title: monocytes from healthy donor HD2, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223458


title: L3a2 DNA rep1

description: Library name: L3a2 DNA rep1


title: Rgs14 KO, sample 1, HTO

description: Library name: Sample1_HTO

value: KO


title: monocytes from healthy donor HD2, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223457

value: Vehicle


title: Rgs14 KO, sample 2, HTO

description: Library name: Sample2_HTO


title: Bcat_GOF_day3

description:
Library name: Sample 2
10X Genomics


title: L3a1 RNA rep2

description: Library name: L3a1 RNA rep2


title: Control 1

description:
Library name: Sample 1
10X Genomics


title: monocytes from healthy donor HD1, M2-like, LPS

description: Library name: BSSE_QGF_223456


title: L3a1 DNA rep2

description: Library name: L3a1 DNA rep2


title: L4a1 Barcode-oligonucleotide

description: Library name: L4a1 Barcode-oligonucleotide

organism: synthetic construct

source_name: plasmid library

value: plasmid library


title: L3a1 RNA rep1

description: Library name: L3a1 RNA rep1


title: Control, sample 3, GEX

description: Library name: Sample3_GEX


title: monocytes from healthy donor HD1, M2-like, Vehicle

description: Library name: BSSE_QGF_223455


title: monocytes from healthy donor HD1, M1-like, Vehicle

description: Library name: BSSE_QGF_223453


title: L3a1 DNA rep1

description: Library name: L3a1 DNA rep1


title: monocytes from healthy donor HD1, M1-like, LPS

description: Library name: BSSE_QGF_223454


title: L3a3 Barcode-oligonucleotide

description: Library name: L3a3 Barcode-oligonucleotide


title: Rgs14 KO, sample 1, GEX

description: Library name: Sample1_GEX


title: L3a2 Barcode-oligonucleotide

description: Library name: L3a2 Barcode-oligonucleotide


title: L2a3 DNA rep3

description: Library name: L2a3 DNA rep3


title: L3a1 Barcode-oligonucleotide

description: Library name: L3a1 Barcode-oligonucleotide


title: L2a3 RNA rep3

description: Library name: L2a3 RNA rep3


title: Rgs14 KO, sample 2, GEX

description: Library name: Sample2_GEX


title: L2a3 Barcode-oligonucleotide

description: Library name: L2a3 Barcode-oligonucleotide


title: Pax6het

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

description: Library name: Pax6het

data_processing:
follow the protocol from 10X genomics
Assembly: GRCm38.91
Supplementary files format and content: matrix file

source_name: cornea/limbus

extract_protocol:
Whole eyes were harvested . The lens, retina, iris, and trabecular network were removed leaving the entire ocular anterior segment, from which most of the conjunctiva was carefully dissected and discarded. Dissect corneas with ice cold PBS and put corneas into one Eppendorf tube filled with 0.7mg/mL liberase TM (from Roche) in RPMI.  Place tube in 37 degree incubator with 5% CO2 for 1 hour. Then add 500ul 0.25%Trypsin for 15min. Use 40um filter into Eppendorf tube. Cell viability was checked and accepted with at least an 80% viability score. Such cells were processed for scRNA-seq using 10XGenomics pipeline in the Northwestern University NUseq Core.
follow the instructions from 10XGenomics

value: cornea/limbus


title: L2a2 Barcode-oligonucleotide

description: Library name: L2a2 Barcode-oligonucleotide


title: monocytes from healthy donor HD1, undifferentiated M0, Vehicle

description: Library name: BSSE_QGF_223451


title: L2a3 RNA rep2

description: Library name: L2a3 RNA rep2


title: Control, sample 4, GEX

description: Library name: Sample4_GEX


title: wt

description: Library name: wt

value: wt


title: monocytes from healthy donor HD1, undifferentiated M0, LPS

description: Library name: BSSE_QGF_223452


title: L2a1 Barcode-oligonucleotide

description: Library name: L2a1 Barcode-oligonucleotide


title: ICI-associated myocarditis rescued,  batch 2

city: Houston

first: Yuanyuan

last: Zhu

state: Texas

address: 6565 Fannin St

department: Systems Medicine and Bioengineering

institute: Houston Methodist

description:
Library name: WO_66096
ICI-associated myocarditis was successfully de novo mitigated by IL-17A neutralizing antibody

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files (v2.0.0).
Reads were mapped to the mouse reference transcriptome (mm10). Spatial barcodes and UMIs were used to generate feature-barcode matrices.
Further normalization and clustering were performed using Seurat (v5.1.0) in R.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene/probe IDs and names
Supplementary files format and content: matrix.mtx.gz: gene expression matrix in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg: image of aligned fiducial markers
Supplementary files format and content: detected_tissue_image.jpg: image of tissue section with detected spots
Supplementary files format and content: scalefactors_json.json: JSON file containing image scale factors
Supplementary files format and content: tissue_hires_image.png: high-resolution tissue image
Supplementary files format and content: tissue_lowres_image.png: low-resolution tissue image
Supplementary files format and content: tissue_positions.csv: spatial barcode coordinates and tissue detection flags
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
FFPE heart tissues were sectioned at 5 μm thickness and mounted on 10x Genomics Visium Spatial Gene Expression slides. Slides were baked at 60°C overnight, deparaffinized with xylene and ethanol gradients, followed by H&E staining prior to spatial transcriptomics workflow.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Heart

value: wild type

value: anti-PD-1 + anti-CTLA-4 + IL-17A neutralizing antbody


title: L2a3 RNA rep1

description: Library name: L2a3 RNA rep1


title: Human_6

city: University of Sydney

first: Lipin

last: Loo

state: New South Wales

address: CHARLES PERKINS CENTRE D-17,

department: Charles Perkins Centre and School of Life & Environmental Sciences

country: Australia

institute: The University of Sydney

description:
Library name: sample7
10X Genomics

data_processing:
Generated sequences were aligned with 10X Genomics Space Ranger version 2.0.0 with mm10-2020-A as reference, before downstream analysis with Seurat and RCTD.
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Lumbar spinal cord

extract_protocol:
Sham lumbar spinal cord were obtained from mice and snap frozen in liquid nitrogen before embedding in OCT. Embedded tissues were sectioned at 10um before placement within fiducial frames of 6.5mm x 6.5mm capture areas on a Visium Spatial glass slide. These sections then undergo H&E staining (MethanolFixationandHEStaining_RevB), followed by imaging on a Leica DM6B and at 10x magnification.
Imaged sections are permeabilized, reverse-transcribed before denaturation. The collected cDNA are further amplified and indexed before sequencing to achieve 75 million reads, which equated to approximately 42,501 reads per spot for the presented data.

value: Lumbar spinal cord

value: Neurons  and non-neuronal nuclei

value: WT

value: Healthy


title: Human_8

description:
Library name: sample8
10X Genomics


title: L2a3 DNA rep2

description: Library name: L2a3 DNA rep2


title: L1a3 Barcode-oligonucleotide

description: Library name: L1a3 Barcode-oligonucleotide


title: Human_4

description:
Library name: sample6
10X Genomics


title: L2a3 DNA rep1

description: Library name: L2a3 DNA rep1


title: ICI-assocaited myocarditis, batch 2

description:
Library name: WO_66094
ICI-associated myocarditis developped in this group

value: anti-PD-1 + anti-CTLA-4


title: L1a2 Barcode-oligonucleotide

description: Library name: L1a2 Barcode-oligonucleotide


title: Human_2

description:
Library name: sample5
10X Genomics


title: ICI-associated myocarditis rescued,  batch 1

description:
Library name: WO_66095
ICI-associated myocarditis was successfully de novo mitigated by IL-17A neutralizing antibody


first: Xiang

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: CKDL240027297_CKDL240027299_m323_LysM_cre_Female_2
cellranger demultiplexed

data_processing:
We utilized the cellranger pipeline for processing the multiplexed raw data. In each dataset and for every patient, we generated multiplexing and count assays based on CellRanger outputs, with all subsequent steps performed using Seurat packages.
Assembly: GFP_mm10_genome.fa
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: bone metastasis

extract_protocol:
Tissues were minced and homogenized in 24-well plates using scalpels and pestles, with 0.5 ml of DMEM. Subsequently, 1 ml of tissue dissociation buffer was added, and the mixture was incubated at 37°C for 45 minutes. The dissociation solution was prepared by dissolving collagenase A (Sigma, 11088793001) in a mixture of 75% (vol/vol) DMEM F12/HEPES medium (Gibco, 113300) and 25% (vol/vol) BSA fraction V (Gibco, 15260037) to achieve a working concentration of 1 mg ml⁻¹. The resulting tissue suspension was filtered through a 70-μm strainer to ensure complete homogenization, and the strainer was rinsed with DMEM to recover any remaining single cells. The flow-through was then centrifuged at 500g for 5 minutes, and the supernatant was carefully decanted. In cases where red blood cells (RBCs) were present, a 1×RBC lysis buffer (1:10 dilution of 10× RBC lysis buffer (MACS, 130-094-183) in Milli-Q water) was applied and incubated at room temperature for 10 minutes. To halt and remove RBC lysis, 20 ml of DMEM was added, and the mixture was centrifuged at 450g for 5 minutes. The supernatant was discarded, and the cell pellet was washed with 10 ml of cold DMEM at 4°C. After another centrifugation at 500g for 5 minutes, the supernatant was removed, and the cells were resuspended in cold PBS (Sigma, D8537) containing 0.04% BSA. Finally, the cell suspension was passed through a 40-μm flowmi cell strainer to ensure uniformity.
Library construction follows CellPlex and TotalSeqC sample multiplexing protocal, for CellPlex multiplexed sample, we used 3' end sequencing protical, while we used 5' end sequencing for TotalSeqC multiplexed samples.

value: Female

value: bone metastasis

value: LysM-cre


title: liver, control, CT44, replicate 1, female

city: Manchester

first: Jessica

middle: Minnie

last: Treeby

address: Oxford Road

institute: Manchester University

description: Library name: JMF79_S79_R1_001

data_processing:
Gencode Release M38 (GRCm39)
The Galaxy server was used for all pipelines except DryR and Masigpro. Raw reads were QCed and trimmed using Trimmomatic (Sliding window trimming, 4 bases average, average quality required 20) before being aligned to the mouse genome (Release M38 GRCm39) using HISAT2 using default options. Transcripts were assembled and counted using feature counts with GENCODE annotations for M38 (GRCm39), using default options and keeping all annotated genes including all predicted genes, pseudogenes and non-coding RNAs. Pairwise comparisons of transcriptome signatures were performed for each timepoint, with diet (ad libitium fed and fasting) as primary factor and sex (male or female) as the secondary factor using DEseq2 or DEXseq for gene and exon counts, respectively. Exon usage values equal to 0 were replaced by the smallest non-zero exon usage value (a, floor value), exon usage values equal to 1 were replaced by 1-a (ceiling value), and exon usage values equal to 0.5 were replaced by 0.4999999. To satisfy the Gaussian assumptions of the linear modeling frameworks in both maSigPro and dryR, exon usage proportions were logit-transformed (LN(exon usage/1-exon usage)). Lastly, a variance-based filter was applied where exons with >40 floor/ceiling values were discarded. Low expression genes/exons i.e., genes/exons with less than 10 counts per 20 samples (1/4 of the dataset) were filtered out in R before analyses with DryR and MaSigPro. Genes were further filtered in DryR and Masigpro based on BICW values (>0.8) or p values (<0.05), respectively. High confidence differentially expressed genes/exons passed DryR or Masigpro thresholds and DESeq2/DEXseq thresholds (adjusted p value < 0.05, LogFC [1] and adjusted p value < 0.05, LogFC [0.58], respectively) in at least two time points.
Assembly: Release M38 (GRCm39)
Supplementary files format and content: Normalised count file provided (.txt format)

source_name: Liver

growth_protocol: Animal experiments were licensed under the Animals (Scientific Procedures) Act of 1986 (UK) and were approved by the animal welfare committees at the University of Manchester. Eight- to twelve-weeks old C57BL/6J male and female mice were purchased from Charles River (UK) and acclimatized to the local animal unit for 1 week before the experiment. Mice were provided with a standard chow diet (TD.220157) ad libitum and group-housed (4-4 individuals) under a 12:12 h light/dark cycle at ~350 lux during the light phase and 0 lux during the dark phase for 10 days before being exposed to constant darkness (DD) for the 11th day. Ambient temperature was kept at 21 ± 5 °C, the humidity was ~51 ± 8%, with water available ad libitum.

extract_protocol:
RNA was extracted form liver samples using standard Trizol procedure (Invitrogen).
Total RNA was submitted to the Genomic Technologies Core Facility (GTCF). Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422

treatment_protocol: On the 11th day from CT8 and every 4 hours thereafter until CT44, under dim red light mice were killed humanely by cervical dislocation followed by cessation of circulation. Then, liver ( ~40 mg from the centre of the left lobe) samples were immediately dissected and frozen on dry ice.

value: Liver

value: female

value: control


description:
Library name: CKDL240027297_CKDL240027299_m323_LysM_cre_Female_1
cellranger demultiplexed


title: A375 ADI-1

city: Amsterdam

first: Mrittika

last: Adhikary

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: Sample 3

data_processing:
Alignment to GChr38/hg38 using STAR 2.7.11b
Read counts were extracted using featureCounts 2.0.1
Assembly: hg38
Supplementary files format and content: tab-delimited txt file contains raw counts for each sample

growth_protocol: A375 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin. were maintained in a humidified atmosphere containing 5% CO2 at 37 °C

extract_protocol:
cells were harvested in RLT buffer (Qiagen) and RNA was isolated using the RNeasy Mini Kit (74106, Qiagen), including an on column DNase digestion (79254, Qiagen),  according to the manufactures instructions. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using “Agilent RNA 6000 Nano” (G2938-90034, Agilent Technologies).
Total RNA samples having RIN>8 were subjected to library generation using the TruSeq stranded mRNA library preparation kit, according to the manufacturer's instructions (Document # 1000000040498 v00 , Illumina) with incorporation of xGen UDI-UMI adapters (Integrated DNA Technologies, Inc., Coralville). The stranded mRNA libraries were analyzed on a 2100 Bioanalyzer instrument following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90025, Agilent Technologies), diluted to 10nM and pooled equimolar into multiplex sequencing pools for paired end sequencing on the NovaSeq 6000 Illumina sequencing instrument. Paired-end sequencing was performed using 54 cycles for Read 1, 19 cycles for Read i7, 10 cycles for Read i5 and 54 cycles for Read 2, using the NovaSeq6000 Reagent Kit v1.5 (100 cycles) (20028401, 20028318, Illumina). On average 20M paired reads per sample were generated.

treatment_protocol: Recombinant arginine deiminase (ADI) was used at a final concentration of 250ng/ml. Cells were harvested 48 hours after the start of treatment.

value: Melanoma cancer

value: ADI


title: A375 ctrl-2

description: Library name: Sample 2

value: ctrl


title: L2a2 DNA rep3

description: Library name: L2a2 DNA rep3

value: Fetal chondrocytes


title: L2a2 RNA rep1

description: Library name: L2a2 RNA rep1


title: L2a2 DNA rep2

description: Library name: L2a2 DNA rep2


title: ICI-assocaited myocarditis, batch 1

description:
Library name: WO_66093
ICI-associated myocarditis developped in this group

value: Heart

value: wild type


title: L2a2 RNA rep3

description: Library name: L2a2 RNA rep3


title: liver, control, CT44, replicate 2, male

description: Library name: JMF78_S78_R1_001


title: liver, control, CT44, replicate 1, male

description: Library name: JMF77_S77_R1_001


description:
Library name: CKDL240027297_CKDL240027299_m315_LysM_cre_Female_2
cellranger demultiplexed


title: A375 ADI-2

description: Library name: Sample 4


title: A375 ctrl-1

description: Library name: Sample 1


title: L2a2 RNA rep2

description: Library name: L2a2 RNA rep2


title: liver, control, CT44, replicate 2, female

description: Library name: JMF80_S80_R1_001


title: L1a1 Barcode-oligonucleotide

description: Library name: L1a1 Barcode-oligonucleotide

value: plasmid library


description:
Library name: CKDL240027297_CKDL240027299_m317_LysM_cre_Female_1
cellranger demultiplexed


title: L2a2 DNA rep1

description: Library name: L2a2 DNA rep1


description:
Library name: CKDL240027297_CKDL240027299_m317_LysM_cre_Female_2
cellranger demultiplexed


title: liver, fasted, CT44, replicate 2, female

description: Library name: JMF76_S76_R1_001

value: male


title: Multiplexed Primary and Stem cell-derived islet cells, 1% O2 (0, 6, 24, and 48hrs)

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

description: Library name: Multiplexed Samples

data_processing:
Raw sequencing reads were demultiplexed, aligned to the GRCh38 human reference genome, and UMI-collapsed to generate feature-barcode count matrices using 10x Genomics Cell Ranger v7.1.0.
After initial inspection, all downstream analyses were carried out in R version 4.4.0 using Seurat v5.1.0.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary and stem cell-derived pancreatic islets

growth_protocol: Primary human islets were obtained from a single cadaveric donor. Stem cell-derived islets were generated from the HUES8 human embryonic stem cell line using a multi-stage directed differentiation protocol. All islets were maintained in suspension culture.

extract_protocol:
Islet clusters were dissociated into a single-cell suspension using TrypLE Express, followed by immediate fixation to preserve the transcriptional state, according to 10x's fixed RNA profiling protocol
Libraries were prepared using the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10x Genomics, User Guide CG000527 Rev E).

treatment_protocol: Islet clusters were challenged with acute hypoxia by incubation at 1% O2, 5% CO2 for 0, 6, 24, or 48 hours. Control samples (0 hr) were maintained in normoxia (21% O2, 5% CO2).

value: Primary and HUES8

value: Normoxia vs Hypoxia


description:
Library name: CKDL240027297_CKDL240027299_m315_LysM_cre_Female_1
cellranger demultiplexed


title: liver, fasted, CT44, replicate 1, female

description: Library name: JMF75_S75_R1_001


title: L2a1 RNA rep3

description: Library name: L2a1 RNA rep3


title: L2a1 DNA rep3

description: Library name: L2a1 DNA rep3


title: liver, fasted, CT44, replicate 2, male

description: Library name: JMF74_S74_R1_001


title: Meningioma2_N21-202

city: San Francisco

first: Ayush

last: Aggarwal

address: 1450 3rd St. Helen Diller Family Cancer Research Building

department: Neurosurgery

institute: University of California San Francisco

description:
Library name: NMH-T-1006_Bottom_N21-202
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics SpaceRanger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to generate gene expression counts using SpaceRanger's default settings
Gene expression level of Refseq coding genese were quantified using SpaceRanger's default settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Meningioma

extract_protocol:
Formalin fixed and parafin embedded tissue sections were cut under RNAse free conditions
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slide and Probe kit according to manufacturer's instruction

value: Meningioma


title: Meningioma1_NP21-104

description:
Library name: NMH-T-0280_Top_NP21-104
FFPE Spatial transcriptome sequencing


description:
Library name: CKDL240027297_CKDL240027299_m314_LysM_cre_Male_1
cellranger demultiplexed

value: Male


title: L2a1 RNA rep2

description: Library name: L2a1 RNA rep2


title: liver, fasted, CT44, replicate 1, male

description: Library name: JMF73_S73_R1_001


description:
Library name: CKDL240027297_CKDL240027299_m314_LysM_cre_Male_2
cellranger demultiplexed

value: bone metastasis


description:
Library name: CKDL240027297_CKDL240027299_m313_LysM_cre_Male_2
cellranger demultiplexed

value: LysM-cre


title: liver, control, CT40, replicate 2, female

description: Library name: JMF72_S72_R1_001

value: Liver

value: fasted


title: L2a1 DNA rep2

description: Library name: L2a1 DNA rep2


title: U-2 OS, miniSOG-NES, 5hr poly(I:C) and 3hr SB2960, Enrich, rep2

city: Beijing

first: Songrui

last: Zhao

address: 292 Chengfu Road, Haidian District

institute: Peking University

description:
Library name: SB2960_NES_rep2
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_NES_enrich_rep2

data_processing:
Sequencing reads were firstly processed with Cutadapt (v.1.18) to remove adaptors (adaptor1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adaptor2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Trimmed reads were mapped against the corresponding genome assemblies using hisat2 (v.2.1.0).
Number of reads mapped to each gene was counted with HTSeq (v0.7.2) (-s no)
Differential expression analysis was carried out by DESeq2 (v.1.16.1)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Excel tables include raw counts for each sample.

source_name: U-2 OS

growth_protocol: U-2 OS cells were cultured in McCoy's 5A medium supplemented with 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C with 5% CO2.

extract_protocol:
Cells were lyzed with TRIzol. Total RNAs were extracted, clicked with biotin handles, enriched with streptavidin-coated beads, and purified again with TRIzol. For the study of cancer cell migration, cells with strong biotin signals were sorted by flow cytometry and lyzed with 0.5% (v/v) Triton X-100 and 0.1 U DNase I.
For the profiling of subcellular transcriptomes, less than 100 ng Input RNA samples or 5 μL Enrich RNA samples were utilized for NGS library construction. NEBNext Ultra II RNA Library Prep Kit for Illumina was used for NGS library construction. RNAs were fragmentated to ~300 nt before first strand synthesis. Libraries were sequenced to a depth of 15 G raw base.

treatment_protocol: U-2 OS cells were cultured until the confluence reached 90% for drug treatment. Cells were first incubated in complete medium containing 1.25 μg/mL poly(I:C) for  hr, followed by 2 hr 40 min incubation in either 0.5% DMSO or 20 μM SB2960 containing medium. After rinsing cells once with HBSS, cells incubated with 10 mM propargylamine (PA) and 0.5% DMSO/20 μM SB2960 in HBSS for 5 min, and irradiated with blue light for 15 min.

value: U-2 OS

value: osteosarcoma cells

value: miniSOG-NES

value: 5hr incubation in 1.25 μg/mL poly(I:C) and 3hr in 20 μM SB2960


title: liver, control, CT40, replicate 1, female

description: Library name: JMF71_S71_R1_001

value: female


description:
Library name: CKDL240027297_CKDL240027299_m313_LysM_cre_Male_1
cellranger demultiplexed


title: L2a1 RNA rep1

description: Library name: L2a1 RNA rep1

value: Fetal chondrocytes


title: U-2 OS, miniSOG-NES, 5hr poly(I:C) and 3hr SB2960, Enrich, rep1

description:
Library name: SB2960_NES_rep1
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_NES_enrich_rep1


title: L1a3 RNA rep3

description: Library name: L1a3 RNA rep3


description:
Library name: CKDL240027297_CKDL240027299_m311_LysM_cre_Male_2
cellranger demultiplexed


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, omit PA, Enrich, rep2

description:
Library name: SB2960_G3BP1_-PA_rep2
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_-PA_enrich_rep2


title: U-2 OS, miniSOG-NES, 5hr poly(I:C) and 3hr SB2960, Enrich, rep3

description:
Library name: SB2960_NES_rep3
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_NES_enrich_rep3


title: liver, control, CT40, replicate 2, male

description: Library name: JMF70_S70_R1_001


description:
Library name: CKDL240027296_CKDL240027298_m324_LysM_ctrl_Male_2
cellranger demultiplexed

value: LysM-ctrl


title: liver, control, CT40, replicate 1, male

description: Library name: JMF69_S69_R1_001


description:
Library name: CKDL240027297_CKDL240027299_m311_LysM_cre_Male_1
cellranger demultiplexed


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, omit PA, Enrich, rep1

description:
Library name: SB2960_G3BP1_-PA_rep1
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_-PA_enrich_rep1


title: L2a1 DNA rep1

description: Library name: L2a1 DNA rep1


title: liver, fasted, CT40, replicate 2, female

description: Library name: JMF68_S68_R1_001


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, Input, rep2

description:
Library name: SB2960_G3BP1_+PA_rep2_input
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_G3BP1_input_rep2


title: L1a3 RNA rep2

description: Library name: L1a3 RNA rep2


description:
Library name: CKDL240027296_CKDL240027298_m324_LysM_ctrl_Male_1
cellranger demultiplexed


title: L1a3 DNA rep3

description: Library name: L1a3 DNA rep3


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, Input, rep3

description:
Library name: SB2960_G3BP1_+PA_rep3_input
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_G3BP1_input_rep3


title: liver, fasted, CT40, replicate 1, female

description: Library name: JMF67_S67_R1_001


title: liver, fasted, CT40, replicate 2, male

description: Library name: JMF66_S66_R1_001


title: L1a3 RNA rep1

description: Library name: L1a3 RNA rep1


title: L1a3 DNA rep2

description: Library name: L1a3 DNA rep2


description:
Library name: CKDL240027296_CKDL240027298_m320_LysM_ctrl_Male_2
cellranger demultiplexed


title: liver, fasted, CT40, replicate 1, male

description: Library name: JMF65_S65_R1_001


title: L1a3 DNA rep1

description: Library name: L1a3 DNA rep1


title: liver, control, CT36, replicate 2, female

description: Library name: JMF64_S64_R1_001

value: control


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, Input, rep1

description:
Library name: SB2960_G3BP1_+PA_rep1_input
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_G3BP1_input_rep1


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, Enrich, rep2

description:
Library name: SB2960_G3BP1_+PA_rep2_enrich
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_G3BP1_enrich_rep2


description:
Library name: CKDL240027296_CKDL240027298_m320_LysM_ctrl_Male_1
cellranger demultiplexed


description:
Library name: CKDL240027296_CKDL240027298_m309_LysM_ctrl_Female_2
cellranger demultiplexed

value: Female


title: L1a2 DNA rep3

description: Library name: L1a2 DNA rep3


title: liver, control, CT36, replicate 1, female

description: Library name: JMF63_S63_R1_001


description:
Library name: CKDL240027296_CKDL240027298_m309_LysM_ctrl_Female_1
cellranger demultiplexed


description:
Library name: CKDL240027296_CKDL240027298_m319_LysM_ctrl_Male_2
cellranger demultiplexed


title: L1a2 RNA rep2

description: Library name: L1a2 RNA rep2


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, Enrich, rep1

description:
Library name: SB2960_G3BP1_+PA_rep1_enrich
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_G3BP1_enrich_rep1


title: U-2 OS, miniSOG-NES, 5hr poly(I:C) and 3hr 0.5%DMSO, Enrich, rep3

description:
Library name: polyIC_NES_rep3
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_NES_enrich_rep3

value: 5hr incubation in 1.25 μg/mL poly(I:C) and 3hr in 0.5% DMSO


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr SB2960, Enrich, rep3

description:
Library name: SB2960_G3BP1_+PA_rep3_enrich
Column name in polyIC_SB2960_allcounts.xlsx: SB2960_G3BP1_enrich_rep3


description:
Library name: CKDL240027296_CKDL240027298_m319_LysM_ctrl_Male_1
cellranger demultiplexed


title: liver, control, CT36, replicate 2, male

description: Library name: JMF62_S62_R1_001


title: U-2 OS, miniSOG-NES, 5hr poly(I:C) and 3hr 0.5%DMSO, Enrich, rep2

description:
Library name: polyIC_NES_rep2
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_NES_enrich_rep2


title: L1a2 RNA rep3

description: Library name: L1a2 RNA rep3


title: L1a2 DNA rep2

description: Library name: L1a2 DNA rep2


title: liver, control, CT36, replicate 1, male

description: Library name: JMF61_S61_R1_001


title: U-2 OS, miniSOG-NES, 5hr poly(I:C) and 3hr 0.5%DMSO, Enrich, rep1

description:
Library name: polyIC_NES_rep1
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_NES_enrich_rep1


description:
Library name: CKDL240027296_CKDL240027298_m307_LysM_ctrl_Female_2
cellranger demultiplexed


title: liver, fasted, CT36, replicate 2, female

description: Library name: JMF60_S60_R1_001

value: male


title: L1a2 RNA rep1

description: Library name: L1a2 RNA rep1


title: L1a2 DNA rep1

description: Library name: L1a2 DNA rep1


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, omit PA, Enrich, rep2

description:
Library name: polyIC_G3BP1_-PA_rep2
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_-PA_enrich_rep2


title: liver, fasted, CT36, replicate 1, female

description: Library name: JMF59_S59_R1_001


description:
Library name: CKDL240027296_CKDL240027298_m307_LysM_ctrl_Female_1
cellranger demultiplexed


title: liver, fasted, CT36, replicate 2, male

description: Library name: JMF58_S58_R1_001


description:
Library name: CKDL240027296_CKDL240027298_m306_LysM_ctrl_Female_2
cellranger demultiplexed


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, omit PA, Enrich, rep1

description:
Library name: polyIC_G3BP1_-PA_rep1
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_-PA_enrich_rep1


description:
Library name: CKDL240027296_CKDL240027298_m306_LysM_ctrl_Female_1
cellranger demultiplexed


title: e12.5_Wt1CreER_DTA_slide_seq

description:
Library name: e12.5_Wt1CreER_DTA_slide_seq
e12.5_Wt1CreER_DTA_slide_seq

data_processing:
We acquired the unfiltered feature-barcode matrix for each sample by using Space Ranger (v2. 1. 0) ‘count’ command with manually selected dots and reorient-images enabled) on the demultiplexed FASTQ files and associated image, along with the prebuilt mm10 genome reference 2020-A. After it detected tissue, aligned reads, generated feature-spot matrices, and positioned spots, we then used Seurat for all further analyses. In each slide, Seurat objects were created by Load10X_Spatial function and then normalized with natural-log transformation using log1p. Similarly, we obtained the unfiltered matrix of curioseq data by using Curio seeker (v2.0) with custom GRCm38 genome reference (add eGFP). Specifically, Curio seeker was first used to extract bead and molecular barcodes for the raw FASTQ files of each sample and filter beads obtained from sequencing data against the bead barcode whitelist. After filtering out beads with Hamming distance greater than 2 and creating new seurat object, we manually normalized counts with natural log.
We splitted out the Visium image which has more than one tissue. This process can facilitate the integration with scRNA-seq dataset in later section. We cut segments based on exact positions. After subsetting, we can visualize the certain stage cells either on the full image, or a cropped image. (Stage E11.5, P0, E14.5, E16.5 have two tissues in one image, E17_E11 and P2_E14 from second experiment have three tissues in same image.) In Curio seq samples, we first set filter range of each coordinate and then store the shrank image in a new Seurat object.
Assembly: GRCm38
Supplementary files format and content: rds
Library strategy: Spatial Transcriptomics

value: heart

value: cardiac cells

value: tamoxifen


title: L1a1 DNA rep3

description: Library name: L1a1 DNA rep3


title: liver, fasted, CT36, replicate 1, male

description: Library name: JMF57_S57_R1_001


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, Input, rep3

description:
Library name: polyIC_G3BP1_+PA_rep3_input
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_G3BP1_input_rep3


title: liver, control, CT32, replicate 2, female

description: Library name: JMF56_S56_R1_001


title: e14.5_2_slide_seq

description:
Library name: e14.5_2_slide_seq
e14.5_2_slide_seq


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, Input, rep2

description:
Library name: polyIC_G3BP1_+PA_rep2_input
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_G3BP1_input_rep2


title: liver, control, CT32, replicate 2, male

description: Library name: JMF54_S54_R1_001


title: L1a1 RNA rep2

description: Library name: L1a1 RNA rep2


title: L1a1 RNA rep1

description: Library name: L1a1 RNA rep1


title: e14.5_1_slide_seq

description:
Library name: e14.5_1_slide_seq
e14.5_1_slide_seq


title: e13.5_2_slide_seq

description:
Library name: e13.5_2_slide_seq
e13.5_2_slide_seq

value: CD1 wildtype


title: L1a1 DNA rep2

description: Library name: L1a1 DNA rep2


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, Enrich, rep3

description:
Library name: polyIC_G3BP1_+PA_rep3_enrich
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_G3BP1_enrich_rep3


title: liver, control, CT32, replicate 1, female

description: Library name: JMF55_S55_R1_001

value: Liver


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, Enrich, rep2

description:
Library name: polyIC_G3BP1_+PA_rep2_enrich
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_G3BP1_enrich_rep2


title: e13.5_1_slide_seq

description:
Library name: e13.5_1_slide_seq
e13.5_1_slide_seq


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, Input, rep1

description:
Library name: polyIC_G3BP1_+PA_rep1_input
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_G3BP1_input_rep1


title: liver, control, CT32, replicate 1, male

description: Library name: JMF53_S53_R1_001

value: fasted


title: U-2 OS, G3BP1-miniSOG, 5hr poly(I:C) and 3hr 0.5%DMSO, Enrich, rep1

description:
Library name: polyIC_G3BP1_+PA_rep1_enrich
Column name in polyIC_SB2960_allcounts.xlsx: polyIC_G3BP1_enrich_rep1

value: U-2 OS


title: liver, fasted, CT32, replicate 2, female

description: Library name: JMF52_S52_R1_001


title: e12.5_2_slide_seq

description:
Library name: e12.5_2_slide_seq
e12.5_2_slide_seq


title: liver, fasted, CT32, replicate 1, female

description: Library name: JMF51_S51_R1_001