title: DSP-1001660014867-C-D06

description: Library name: Sample 186


title: ACC_ELA_SAFit2_NoInteraction_103

status: Public on Jul 15 2026

type: SRA

city: Solna

first: Juan Pablo

last: Lopez

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: Library name: 22L006230

library_source: transcriptomic

data_processing:
Sequence reads were processed using the nf-core RNA-seq pipeline (nf-core/rnaseq v3.6). Adapter trimming and quality control were performed using the default parameters.
Trimmed reads were aligned to the reference genome using STAR within the nf-core/rnaseq workflow, with Gencode M30 gene annotaion.
Gene-level read counts were generated based on Gencode M30 annotation. Strand-specific information was specified as reverse-stranded.
VST was performed using DESeq2 for downstream analysis. Duplicate read analysis (DupRadar) and library complexity estimation (Preseq) were skipped as specified in the pipleline options.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text files containing gene-level raw read counts for 246 RNA-seq samples

molecule: polyA RNA

organism: Mus musculus

source_name: anterior cingulate cortex

extract_protocol:
Total RNA was isolated from punches using the miRNeasy Mini Kit (QIAGEN, Venlo, NL; cat. No. 1038703) according to the manufacturer's instructions, using Rnase-free technique throughout. After RNA isolation, RNA integrity number (RIN) was measured using the Agilent 2100 Bioanalyzer system and quantified by Qubit (Thermo Fisher Scientific). RNAs with a RIN value >7 were selected for mRNA sequencing (poly-A selected).
The libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (Illumina), following the kit's instructions.

tag: tissue

value: anterior cingulate cortex

tag: treatment


title: DSP-1001660014867-C-D03

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

country: USA

institute: UT Southwestern Medical Center

description: Library name: Sample 183

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw read counts in DCC
Supplementary files format and content: RNA_Q3_normalied_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

molecule: total RNA

organism: Homo sapiens

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction

tag: panel (wta_+ipa)

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: IA

tag: scan name

tag: roi

tag: segment

value: Desmin


title: ACC_ELA_Vehicle_SocialInteraction_59

description: Library name: 22L006229


title: DSP-1001660014867-C-D02

description: Library name: Sample 182


title: ACC_ELA_Vehicle_NoInteraction_5

description: Library name: 22L006228


title: PFC_ELA_SAFit2_SocialInteraction_55

description: Library name: 22L006227

source_name: medial prefrontal cortex

value: medial prefrontal cortex


title: DSP-1001660014867-C-C12

description: Library name: Sample 180


title: DSP-1001660014867-C-D01

description: Library name: Sample 181


title: PFC_Ctrl_Vehicle_NoInteraction_9

description: Library name: 22L005578


title: DSP-1001660014867-C-C11

description: Library name: Sample 179


title: RNA_3D-iMac_day19_Rep3

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

country: China

institute: Tsinghua University

data_processing:
For RNA-seq, reads were trimmed using TrimGalore software (version 0.4.4) with default settings. Subsequently, the adaptor-trimmed paired-end RNA-Seq reads were aligned to the hg38 whole genome employing hisat2 with the -p16 parameter. Read counts were determined by utilizing htseq-count (version 0.11.1) and specifying the following parameters: -r pos -a 10 -t exon -s no -i gene_id -m union. Normalization of raw data counts and identification of differentially expressed genes were carried out with the aid of DESeq2 software, adhering to specific criteria (|log2fc| ≥ 1 and false discovery rate [FDR] ≤ 0.05). For ATAC-seq, all paired-end raw reads underwent processing with TrimGalore (version 0.4.4) to eliminate adapters and low-quality sequences. The adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq data were then aligned to the hg38 genome using bowtie2 (version 2.3.5) 52, employing the following parameters: --t --q --N 1 --L 25. PCR duplicates and multiply mapped reads were subsequently removed by utilizing Picard tools MarkDuplicates (available at https://broadinstitute.github.io/picard/). Following this, replicate BAM files for each time point were consolidated, and reads aligning to blacklisted genomic regions were discarded prior to peak calling with MACS253 (version 2.2.6). The enriched transcription factor motifs were analyzed using Homer (version 4.10.4, findMotifsGenome). Additionally, signal tracks for each sample were created with the bamCoverage function from deeptools and normalized to Reads Per Kilobase Million (RPKM) for ease of visualization.
Assembly: GRCh38
Supplementary files format and content: For single-cell datasets, processed data are UMI matrix and cell barcodes produced by Cellranger pipeline.
Supplementary files format and content: bw

extract_protocol:
Total RNA were extracted by TRIZol.
RNA-seq library were prepared according to SMART-seq2 protocol. ATAC-seq library were prepared according to the omni-ATAC-seq protocol.  CHIP-seq library were prepared according an ultra-low-input native ChIP-seq protocol.Single-cell libraries were prepared according to 10X genomics' manual.

tag: cell line

tag: cell type

value: macrophage

tag: time point

tag: protocol


title: PFC_ELA_SAFit2_NoInteraction_15

description: Library name: 22L005579


title: DSP-1001660014867-C-C10

description: Library name: Sample 178


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-090

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-090_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B4-A4_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B4-A4.bw

library_source: genomic

data_processing:
Illumina NGS adapter trimming (cutadapt)
DamID PCR adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
alignment to Lambda phage genome (bowtie2)
count reads into GATC tiles of human genome (htseq-count)
spike-in correction, coverage-normalization (FPKM), background subtraction, and binning (analyzeRaPID)
Assembly: hg38
Supplementary files format and content: bigWig with RaPID-FPKM normalization at 5kbps and/or 25kbps binning
Library strategy: DamID-Seq

molecule: genomic DNA

source_name: blood

growth_protocol: RPMI 1640 base media supplemented to 10% with fetal bovine serum (tetracycline-screened), GlutaMAX, 1X PenStrep, 1ug/mL puromycin. Cells were cultured at +37C in 5%CO2 in log phase growth.

extract_protocol:
genomic DNA
RaPID-labelled fragments were enriched per the DamID PCR protocol with methylated Lambda gDNA spike-in.
Enriched DNA fragments (200-2000bps) were then sheared to 300-600bps.
NGS libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: pre-treatment with doxycycline (20-24h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with Shield1 treatment  wherein siRNA is used, pretreated at -2d prior to CRISPR/Cas9 Nucleofection and again simultaneously with CRISPR/Cas9 Nucleofection.

value: blood

value: myelogenous leukemia

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-090

tag: batch


title: PFC_ELA_Vehicle_NoInteraction_43

description: Library name: 22L005577


title: DSP-1001660014867-C-C09

description: Library name: Sample 177


title: DSP-1001660014867-C-C08

description: Library name: Sample 176


title: PFC_ELA_Vehicle_SocialInteraction_93

description: Library name: 22L005576


title: PFC_Ctrl_Vehicle_NoInteraction_41

description: Library name: 22L005575


title: DSP-1001660014867-C-C07

description: Library name: Sample 175


title: DSP-1001660014867-C-C06

description: Library name: Sample 174


title: PFC_ELA_SAFit2_SocialInteraction_95

description: Library name: 22L005574


title: PFC_Ctrl_Vehicle_SocialInteraction_57

description: Library name: 22L005573


title: DSP-1001660014867-C-C05

description: Library name: Sample 173


title: RNA_3D-iMac_day16_Rep3


title: PFC_ELA_Vehicle_NoInteraction_99

description: Library name: 22L005572


title: DSP-1001660014867-C-C03

description: Library name: Sample 171


title: PFC_ELA_Vehicle_SocialInteraction_91

description: Library name: 22L005571


title: PFC_Ctrl_Vehicle_SocialInteraction_105

description: Library name: 22L005569


title: DSP-1001660014867-C-C01

description: Library name: Sample 169

value: PF


title: PFC_ELA_SAFit2_NoInteraction_47

description: Library name: 22L005570


title: PFC_ELA_Vehicle_SocialInteraction_21

description: Library name: 22L005568


title: DSP-1001660014867-C-C04

description: Library name: Sample 172


title: DSP-1001660014867-C-C02

description: Library name: Sample 170


title: DSP-1001660014867-C-B12

description: Library name: Sample 168


title: DSP-1001660014867-C-B11

description: Library name: Sample 167


title: PFC_Ctrl_Vehicle_NoInteraction_97

description: Library name: 22L005566


title: PFC_ELA_Vehicle_NoInteraction_101

description: Library name: 22L005567


title: DSP-1001660014867-C-B10

description: Library name: Sample 166


title: DSP-1001660014867-C-B09

description: Library name: Sample 165


title: PFC_ELA_SAFit2_SocialInteraction_31

description: Library name: 22L005565


title: PFC_ELA_SAFit2_NoInteraction_71

description: Library name: 22L005564


title: PFC_Ctrl_Vehicle_SocialInteraction_25

description: Library name: 22L005563


title: PFC_ELA_Vehicle_NoInteraction_13

description: Library name: 22L005562


title: DSP-1001660014867-C-B06

description: Library name: Sample 162


title: DSP-1001660014867-C-B08

description: Library name: Sample 164


title: DSP-1001660014867-C-B05

description: Library name: Sample 161


title: PFC_ELA_SAFit2_NoInteraction_87

description: Library name: 22L005561


title: PFC_ELA_Vehicle_SocialInteraction_53

description: Library name: 22L005560


title: DSP-1001660014867-C-B04

description: Library name: Sample 160


title: PFC_Ctrl_Vehicle_NoInteraction_65

description: Library name: 22L005558


title: DSP-1001660014867-C-B01

description: Library name: Sample 157


title: DSP-1001660014867-C-B02

description: Library name: Sample 158


title: PFC_ELA_SAFit2_SocialInteraction_79

description: Library name: 22L005557


title: PFC_Ctrl_Vehicle_SocialInteraction_49

description: Library name: 22L005556


title: PFC_ELA_SAFit2_SocialInteraction_63

description: Library name: 22L005559


title: PFC_ELA_SAFit2_NoInteraction_7

description: Library name: 22L005555


title: DSP-1001660014867-C-A11

description: Library name: Sample 155


title: PFC_Ctrl_Vehicle_NoInteraction_33

description: Library name: 22L005554


title: DSP-1001660014867-C-A10

description: Library name: Sample 154


title: DSP-1001660014867-C-A08

description: Library name: Sample 152


title: PFC_Ctrl_Vehicle_NoInteraction_81

description: Library name: 22L005551


title: PFC_ELA_SAFit2_SocialInteraction_23

description: Library name: 22L005550


title: DSP-1001660014867-C-A07

description: Library name: Sample 151


title: DSP-1001660014867-C-A06

description: Library name: Sample 150


title: PFC_ELA_Vehicle_SocialInteraction_61

description: Library name: 22L005549


title: PFC_ELA_SAFit2_NoInteraction_39

description: Library name: 22L005547


title: ChIP_3D-iMac_day12_K4me3_Rep1

tag: antibody


title: PFC_ELA_Vehicle_NoInteraction_69

description: Library name: 22L005546


title: DSP-1001660014867-C-A02

description: Library name: Sample 146


title: DSP-1001660014867-C-A03

description: Library name: Sample 147


title: PFC_ELA_SAFit2_SocialInteraction_111

description: Library name: 22L005545


title: DSP-1001660014603-D-H12

description: Library name: Sample 145


title: PFC_Ctrl_Vehicle_NoInteraction_1

description: Library name: 22L005543


title: DSP-1001660014603-D-H10

description: Library name: Sample 143


title: PFC_ELA_SAFit2_NoInteraction_103

description: Library name: 22L005542


title: PFC_ELA_Vehicle_SocialInteraction_59

description: Library name: 22L005541


title: DSP-1001660014603-D-H08

description: Library name: Sample 141


title: PFC_ELA_Vehicle_NoInteraction_5

description: Library name: 22L005540


title: DSP-1001660014603-D-H06

description: Library name: Sample 139

source_name: Lupus 2

value: Lupus 2

value: CF


title: Spatial_SedIR_2  Spatial RNA-seq library

city: Manhasset

first: Hai

last: Huang

state: NY

address: 350 community drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

description: Library name: Spatial_liver_SedIR_rep2

data_processing:
Raw reads were assessed for quality using FastQC
Adapter trimming was performed using Trimmomatic
Reads were aligned to the mouse reference genome (mm10) using STAR
Gene counts were quantified using featureCounts
Downstream analysis including normalization and clustering was performed using Seurat (v4.4)
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data files include gene-by-sample count matrices in CSV format

source_name: liver

growth_protocol: Mice were maintained under SPF conditions with a 12-hour light/dark cycle and free access to food and water.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: tissue section

tag: genotype

value: wild-type (WT C57BL/6)

value: ischemia-reperfusion injury (60min ischemia/6h reperfusion)


title: DSP-1001660014603-D-H07

description: Library name: Sample 140

value: DESMIN


title: Spatial_SedIR_1  Spatial RNA-seq library

description: Library name: Spatial_liver_SedIR_rep1


title: DSP-1001660014603-D-H05

description: Library name: Sample 138


title: Spatial_SedSham_1  Spatial RNA-seq library

description: Library name: Spatial_liver_SedSham_rep1

value: sham operation


title: DSP-1001660014603-D-H04

description: Library name: Sample 137

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: Spatial_SedSham_2  Spatial RNA-seq library

description: Library name: Spatial_liver_SedSham_rep2


title: DSP-1001660014603-D-H03

description: Library name: Sample 136


title: SedIR_4 single-cell RNA-seq library

description: Library name: liver_SedIR_rep4

value: CD45+ immune cells


title: SedIR_3 single-cell RNA-seq library

description: Library name: liver_SedIR_rep3


title: DSP-1001660014603-D-H02

description: Library name: Sample 135


title: DSP-1001660014603-D-H01

description: Library name: Sample 134


title: single B. thetaiotaomicron cells at MEP from well A11

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

country: Germany

institute: Helmholtz Insitute

description: Library name: A11

library_source: transcriptomic single cell

data_processing:
Sequence reads were trimmed for Nextera adapter and MATQ-Seq primers using bbmap. bbduk.sh -Xmx10g t=20
Trimmed reads were then mapped to the reference genome using bowtie2 version 2.3.4.1. bowtie2 -p 30
features were assigned using featureCounts.
Read counts extraction was performed using feature counts version 2.0.1
Assembly: GCF_000011065.1
Supplementary files format and content: tab delimited text file contains raw counts for each sample

organism: Bacteroides thetaiotaomicron

growth_protocol: B. thetaiotaomicron cells were grown in tryptone yeast glucose (TYG) media to mid-exponential phase (OD2), anaerobiaclly at 37 degrees.

extract_protocol:
MATQ-Seq and ribosomal RNA depletion with DASH. A single cell was sorted per well of a 96 well plate. Cells were lysed using mechanical sonication. cDNA librairies were obtained using the MATQ-Seq reverse transcription protocol. Ribosomal cDNA was depleted from the cDNA librairies using DASH, optimized for bacteroides thetaiotaomicron.
Library were constructed using the Nextera XT kit from Illumina

treatment_protocol: Fixed in 50% RNAlater

value: WT

value: Fixed in 50% RNAlater


title: SedIR_2 single-cell RNA-seq library

description: Library name: liver_SedIR_rep2


title: DSP-1001660014603-D-G12

description: Library name: Sample 133


title: DSP-1001660014603-D-G10

description: Library name: Sample 131


title: DSP-1001660014603-D-G11

description: Library name: Sample 132


title: Sham_1 single-cell RNA-seq library

description: Library name: liver_SedSham_rep1


title: DSP-1001660014603-D-G09

description: Library name: Sample 130


title: PMs, WT1, VSV 4h

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

description: Library name: WT1

data_processing:
We first apply Stringtie (version: 1.3.0) to count the number of Fragments for each gene after Hisat2 alignment.
Then the TMM (trimmed mean of M values) method was used to standardize the expression levels across various samples.
We then use Perl script to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) value for each gene.
Apply edgeR for differential gene analysis, obtain p-value, and perform multiple hypothesis testing correction. By controlling the FDR (False Discovery Rate) to determine the threshold of p-value, the corrected p-value is q-value. At the same time, we calculate the differential expression multiple, which is Fold change
Genes that exhibit a fold change in expression level larger than 2.0 and a q-value less than 0.05 are referred to as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

source_name: macrophages

growth_protocol: PMs were generated from mice in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit (MagBeads) (Cat#T102096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

treatment_protocol: WT and Rbm25 deficient PMs were infected with vesicular stomatitis virus for 4 hours

value: macrophages

value: PMs

value: Mouse peritoneal macrophages

value: VSV for 4 hours


title: DSP-1001660014603-D-G06

description: Library name: Sample 127

value: PF


title: DSP-1001660014603-D-G05

description: Library name: Sample 126

value: Lupus 2


title: single B. thetaiotaomicron cells at MEP from well D9

description: Library name: D9


title: KO5

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: Library name: SV11-KO5

data_processing:
Fastq files were processed through nf-core/rnaseq pipeline (v1.4.2) with STAR/Salmon combination for mapping and quantification
Assembly: GRCm38 – Ensembl Release 97
Supplementary files format and content: Tab-delimited table with raw counts

source_name: Cortex

extract_protocol:
RNeasy® Plus Mini Kit, 74134, Qiagen
Stranded cDNA libraries were prepared with a NEBNext Ultra II directional RNA library prep kit (E7760, New England Biolabs), according to the manufacturer’s instructions.

treatment_protocol: Cortices from P3 NexCre/+;Cdk7lox/lox;R26EYFP/+ (Cdk7 KO)  and NexCre/+ ;Cdk7+/+ ;R26EYFP/+ (Ctrl) mouse pups were microdissected in ice-cold DPBS-glucose. They were dissociated using a gentleMACS™ instrument with a postnatal neuron dissociation kit (130-094-802, Miltenyi Biotec). The dissociated samples were filtered through a 70 µm strainer rinsed with DPBS containing 0.5% BSA, centrifuged at 300×g for 10 min at room temperature, and the supernatant discarded. The cell pellets were resuspended in 300 µL of phenol red-free HBSS and transferred into 5 mL tubes. Cortical neurons were sorted based on EYFP expression using a FACSAria™ III flow cytometer, harvested in HBSS supplemented with 10% FBS, and centrifuged at 300× g for 7 min at 4°C.  Cell pellets were finally lysed in RLT buffer (from RNeasy® Plus Mini Kit, 74134, Qiagen) completed with 1% 2-mercaptoethanol, and samples were stored at -80°C before RNA extraction.

value: Cortex

value: Cortical projection neurons

value: NexCre/+;Cdk7lox/lox, R26EYFP/+


title: DSP-1001660014603-D-G04

description: Library name: Sample 125


title: KO4

description: Library name: SV10-KO4


title: single B. thetaiotaomicron cells at MEP from well B11

description: Library name: B11


title: DSP-1001660014603-D-G03

description: Library name: Sample 124


title: single B. thetaiotaomicron cells at MEP from well C11

description: Library name: C11


title: KO2

description: Library name: SV8-KO2


title: single B. thetaiotaomicron cells at MEP from well F10

description: Library name: F10


title: DSP-1001660014603-D-G01

description: Library name: Sample 122


title: KO1

description: Library name: SV7-KO1


title: DSP-1001660014603-D-F12

description: Library name: Sample 121


title: CTRL6

description: Library name: SV6-CTRL6

value: NexCre/+;Cdk7+/+, R26EYFP/+


title: single B. thetaiotaomicron cells at MEP from well H6

description: Library name: H6


title: CTRL5

description: Library name: SV5-CTRL5


title: DSP-1001660014603-D-F10

description: Library name: Sample 119

value: IA


title: DSP-1001660014603-D-F09

description: Library name: Sample 118


title: CTRL3

description: Library name: SV3-CTRL3


title: CTRL4

description: Library name: SV4-CTRL4


title: DSP-1001660014603-D-F08

description: Library name: Sample 117


title: DSP-1001660014603-D-F07

description: Library name: Sample 116


title: DSP-1001660014603-D-F06

description: Library name: Sample 115


title: scMultiome_D30_GFPhi_GEX

city: CHICAGO

first: Bin

last: Zhang

state: IL

address: 300 E Superior st., Tarry 4-725

department: Department of Medicine; Hematology/Oncology Division

institute: NORTHWESTERN UNIVERSITY (Feinberg school of medicine)

description:
Library name: D30_GFPhi_GEX
10X Genomics

data_processing:
Raw BCL files were converted and processed using Cell Ranger ARC v2.0.2 (after loading cellranger-arc/2.0.2 and bcl2fastq/2.19.1 modules), and count matrices were generated for each sample (D8_GFPlo, D8_GFPhi, D30_GFPlo, D30_GFPhi, WT, and A2AcKO) using the mm10 reference (refdata-gex-mm10-2020-A) and their corresponding library CSV files.
Assembly: mm10
Supplementary files format and content: Cell Ranger files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: Spleen

growth_protocol: Adora2afl/fl P14 CD45.1+ and LckCre Adora2afl/fl P14 CD45.1+ cells from spleens on day 30 after LCMV Cl13 infection, A2AR-eGFP P14 CD45.1+ from the spleens of mice on day 8 and day 30 after LCMV Cl13 infection were FACS-sorted.

extract_protocol:
Nuclei were isolated and processed using the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit (10x Genomics) according to the manufacturer’s instructions.
Two separate sets of libraries, Gene Expression and ATAC, were generated from each sample, using the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit (10x Genomics) according to the manufacturer’s instructions

value: Spleen

value: P14 CD8+ primary T cells

value: LCMV CL13 infection


title: scMultiome_Adora2ako_GEX

description:
Library name: Adora2ako_GEX
10X Genomics


title: scMultiome_D30_GFPlo_GEX

description:
Library name: D30_GFPlo_GEX
10X Genomics


title: DSP-1001660014603-D-F02

description: Library name: Sample 111

source_name: Lupus 1

value: Lupus 1

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: scMultiome_D8_GFPhi_GEX

description:
Library name: D8_GFPhi_GEX
10X Genomics


title: DSP-1001660014603-D-F01

description: Library name: Sample 110

value: DESMIN


title: scMultiome_D8_GFPlo_GEX

description:
Library name: D8_GFPlo_GEX
10X Genomics


title: DSP-1001660014603-D-E12

description: Library name: Sample 109


title: scMultiome_Adora2ako_ATAC

description:
Library name: Adora2ako_ATAC
10X Genomics

library_source: genomic single cell


title: DSP-1001660014603-D-E11

description: Library name: Sample 108


title: scMultiome_WT_ATAC

description:
Library name: WT_ATAC
10X Genomics


title: DSP-1001660014603-D-E10

description: Library name: Sample 107


title: scMultiome_D30_GFPhi_ATAC

description:
Library name: D30_GFPhi_ATAC
10X Genomics


title: DSP-1001660014603-D-E09

description: Library name: Sample 106


title: scMultiome_D30_GFPlo_ATAC

description:
Library name: D30_GFPlo_ATAC
10X Genomics


title: DSP-1001660014603-D-E08

description: Library name: Sample 105


title: scMultiome_D8_GFPhi_ATAC

description:
Library name: D8_GFPhi_ATAC
10X Genomics


title: DSP-1001660014867-C-B07

description: Library name: Sample 163

value: Desmin


title: DSP-1001660014867-C-B03

description: Library name: Sample 159


title: DSP-1001660014603-D-E07

description: Library name: Sample 104


title: DSP-1001660014867-C-A12

description: Library name: Sample 156


title: scMultiome_D8_GFPlo_ATAC

description:
Library name: D8_GFPlo_ATAC
10X Genomics


title: DSP-1001660014603-D-E06

description: Library name: Sample 103


title: PFC_ELA_Vehicle_NoInteraction_37

description: Library name: 22L005552

value: medial prefrontal cortex


title: PFC_ELA_Vehicle_SocialInteraction_107

description: Library name: 22L005553


title: DSS, biol rep4

city: Zhangjiagang

first: Li

last: Zhou

address: No. 68 West Jiyang Road

institute: The Affiliated Zhangjiagang Hospital of Soochow University

description:
Library name: d4
d4

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to get the raw count.
EdgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: MM10
Supplementary files format and content: This table contains the raw counts and normalized counts for each sample.

source_name: Colon

extract_protocol:
RNA was extracted using mRNA enrichment kit (CloudSeq).
Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions.

treatment_protocol: The mice were fed with water (Control) or 3% DSS in water (DSS) for 7 days

value: Colon

value: DSS


title: DSP-1001660014603-D-E05

description: Library name: Sample 102

value: PF


title: DSP-1001660014603-D-E04

description: Library name: Sample 101


title: DSP-1001660014603-D-E03

description: Library name: Sample 100


title: DSP-1001660014603-D-E02

description: Library name: Sample 99


title: DSS, biol rep1

description:
Library name: d1
d1


title: Control, biol rep4

description:
Library name: c4
c4

value: Control


title: Control, biol rep3

description:
Library name: c3
c3


title: DSP-1001660014603-D-D12

description: Library name: Sample 97


title: DSP-1001660014603-D-D11

description: Library name: Sample 96


title: Control, biol rep1

description:
Library name: c1
c1


title: DSP-1001660014603-D-D10

description: Library name: Sample 95


title: DJACL21_CKDL250005109-1A_22MKTYLT4_S1_L005

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

institute: Dalian medical university

description: Library name: KO3_ATAC

data_processing:
Raw sequencing reads were aligned to the mm39 reference genome using Bowtie2 (v2.3.4.3). Duplicates were removed, and BAM files were filtered to retain uniquely mapped reads. Peaks were called using MACS3 (v3.0.0) with parameters: --nomodel --extsize 200 --shift 100 -q 0.05 --call-summits. Blacklisted regions (ENCODE mm39 blacklist) and non-standard chromosomes were removed using BEDTools (v2.29.1). For quality control, FRiP (Fraction of Reads in Peaks) scores were calculated per sample. Signal tracks were generated using deepTools bamCoverage (v3.5.1) with normalization by sequencing depth (--SPMR) to produce BigWig files for visualization.
Assembly: Mus musculus genome assembly mm39 (GRCm39)
Supplementary files format and content: Processed data include consensus peak sets in BED and narrowPeak formats derived from pooled samples using MACS3. These represent accessible chromatin regions after filtering with the mm39 blacklist. The processed data files are named: ALL_ATAC_final.filt.narrowPeak and ALL_ATAC_summits.bed.

source_name: kidney

extract_protocol:
kidney tissues minced in lysis buffer and performed dounce homogenization to collect nuclei. 50000 nuclei was incubated with Transposition mixture for half-hour at 37 dgree centigrade in a thermal cycler. The DNA fragments were purified by DNA columns MinElute PCR purification kit (QUIAGEN, 28004) and PCR amplified (72 °C; 5 min) and (98 °C; 30 s) followed by 8 cycles of [98 °C; 10 s, 63 °C; 30 s, 72 °C; 1 min] using NEBNext High-Fidelity 2 × PCR Master Kit (M0541L). Sequencing was performed at a minumum depth of 35 million reads per sample on a Novaseq 6000 plotform at the Novagene Corporation Inc, USA (Novogene.com). Standard data processing and analysis was followed as per the methods section in the manuscript.
ATAC-seq libraries were constructed using Tn5 transposase–mediated tagmentation of isolated nuclei, followed by PCR amplification with NEBNext High-Fidelity 2× PCR Master Mix (M0541L). Final libraries were size-selected and purified with MinElute PCR Purification Kit (QIAGEN, 28004). Libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: kidney

value: tubule-specific Acly knockout


title: DSP-1001660014603-D-D09

description: Library name: Sample 94


title: DJ_4_CKDL240025181-1A_227J2LLT4_S1_L005

description: Library name: KO2_ATAC


title: DSP-1001660014603-D-D08

description: Library name: Sample 93


title: DSP-1001660014603-D-D07

description: Library name: Sample 92


title: 8819-DM-1_S1_L005

description: Library name: WT3_ATAC

value: WT


title: DSP-1001660014603-D-D06

description: Library name: Sample 91


title: 8636-AA-2_S1_L005

description: Library name: WT2_ATAC


title: 8636-AA-1_S1_L005

description: Library name: WT1_ATAC


title: DSP-1001660014603-D-D04

description: Library name: Sample 89


title: Primary neural stem cells,RPLP2-Knock down,rRPLP2 cultured,Repeat5

city: 西安市

first: Wu

last: Wei

state: 雁塔区

address: 小寨西路西安交通大学第一附属医院

institute: The First Affiliated Hospital of Xi'an Jiaotong University

description: Library name: shRPLP2_RPLP2_5

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Brain tissue

growth_protocol: Fetal mouse brain tissue (meninges removed) was dissected into 1 mm³ fragments, digested with 0.25% trypsin (37°C, 20 min), and centrifuged (200 × g, 5 min). Cells were expanded in serum-free DMEM/F12 containing: 20 μg/L bFGF, 20 μg/L EGF, 2% B27, 30% glucose, and 1.83 mg/mL heparin. Cultures were passaged every 2–3 days using accutase. At P3, NSPCs were centrifuged (200 × g, 5 min) and differentiated in medium comprising 25% DMEM/F12, 75% neurobasal medium, plus 1% B27 or 0.5% N2.

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: During differentiation, the culture medium was supplemented with the following for subsequent RNA-seq analysis: pAAV-U6-shRNA(Rplp2)-CMV-EGFP-WPRE (2.5 × 10¹² vg/mL), pAAV-U6-shRNA(NC)-CMV-EGFP-WPRE (2.5 × 10¹² vg/mL), rRPLP2 (100 ng/mL), or PBS.

value: Brain tissue

value: neural stem cells

value: RPLP2-Knock down,rRPLP2 cultured


title: DSP-1001660014603-D-D03

description: Library name: Sample 88

value: CONTROL


title: Primary neural stem cells,RPLP2-Knock down,rRPLP2 cultured,Repeat4

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_RPLP2_4


title: DSP-1001660014603-D-D02

description: Library name: Sample 87


title: Primary neural stem cells,RPLP2-Knock down,rRPLP2 cultured,Repeat3

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_RPLP2_3


title: DSP-1001660014603-D-D01

description: Library name: Sample 86


title: Primary neural stem cells,RPLP2-Knock down,rRPLP2 cultured,Repeat2

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_RPLP2_2


title: DSP-1001660014603-D-C12

description: Library name: Sample 85


title: DSS, biol rep3

description:
Library name: d3
d3


title: Primary neural stem cells,RPLP2-Knock down,rRPLP2 cultured,Repeat1

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_RPLP2_1


title: DSS, biol rep2

description:
Library name: d2
d2


title: DSP-1001660014603-D-C11

description: Library name: Sample 84


title: DSP-1001660014603-D-E01

description: Library name: Sample 98


title: Primary neural stem cells,RPLP2-Knock down,Repeat4

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_4

value: RPLP5-Knock down


title: DSP-1001660014603-D-C10

description: Library name: Sample 83


title: Primary neural stem cells,RPLP2-Knock down,Repeat3

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_3

value: RPLP4-Knock down


title: Control, biol rep2

description:
Library name: c2
c2


title: DSP-1001660014603-D-C09

description: Library name: Sample 82

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: Primary neural stem cells,RPLP2-Knock down,Repeat2

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_2

value: RPLP3-Knock down


title: DSP-1001660014603-D-C08

description: Library name: Sample 81


title: Primary neural stem cells,RPLP2-Knock down,Repeat1

address: 小寨西路西安交通大学第一附属医院

description: Library name: shRPLP2_1

value: RPLP2-Knock down


title: DSP-1001660014603-D-C07

description: Library name: Sample 80

value: DESMIN


title: Primary neural stem cells,vector,Repeat3

address: 小寨西路西安交通大学第一附属医院

description: Library name: CON_3

value: vector


title: DSP-1001660014603-D-C06

description: Library name: Sample 79


title: Primary neural stem cells,vector,Repeat2

address: 小寨西路西安交通大学第一附属医院

description: Library name: CON_2


title: DSP-1001660014603-D-C05

description: Library name: Sample 78


title: DSP-1001660014603-D-C04

description: Library name: Sample 77


title: DJ_2_CKDL240025179-1A_227J2LLT4_S1_L005

description: Library name: KO1_ATAC


title: Primary neural stem cells,vector,Repeat1

address: 小寨西路西安交通大学第一附属医院

description: Library name: CON_1


title: AAV8siAATF, replicate 3

city: Mysore

first: Divya

middle: P

last: Kumar

state: Karnataka

address: SS Nagar

department: Biochemistry

country: India

institute: JSS Medical College

description: Library name: siAATF-3

data_processing:
High quality reads were mapped to reference genome using STAR (v.2.7.11.a) and further quantified using FeatureCounts (v2.0.1). Differential expression analysis was carried out using DESeq2 (version 1.42.0) in R (version 4.3.2). Genes with read counts less than 10 across the samples were removed prior to downstream analysis. Raw read counts were normalized by DESeq2. The magnitude (log 2 transformed fold change) and significance (P-value) of differential expression between groups were calculated, and genes with P-values <0.05 were considered as significant. We obtained DEGs with the following criteria: PValue <0.05 and |log 2 fold change|≥2.
Assembly: GRCm39: GCF_000001635.27
Supplementary files format and content: Raw Read Counts per gene and Human and mouse raw counts txt

growth_protocol: Male BALB/c (nu/nu)  mice aged 6 weeks were implated with human HCC cells and observed for the development of HCC.

extract_protocol:
RNA extraction was carried out by All prep DNA/RNA kit (Qiagen). RNA was quantified on a Qubit fluorometer and RIN was obtained using Tapestation 4150 using HS RNA screen tape.
The library preparation was carried out using the SMART-Seq Library Prep Kit

treatment_protocol: After 1 week of tumor implantation, the mice were injected with AAV8-siControl and AAV8-siAATF through the tail vein.

value: liver

value: KD

value: siAATF AAV


title: DSP-1001660014603-D-C03

description: Library name: Sample 76


title: AAV8siAATF, replicate 2

description: Library name: siAATF-2


title: DSP-1001660014867-C-A09

description: Library name: Sample 153

value: IA


title: AAV8 Control, replicate 3

description: Library name: siControl-3

value: control AAV


title: DSP-1001660014603-D-C02

description: Library name: Sample 75


title: AAV8siAATF, replicate 1

description: Library name: siAATF-1


title: DSP-1001660014603-D-C01

description: Library name: Sample 74


title: DSP-1001660014603-D-D05

description: Library name: Sample 90

value: Lupus 1


title: PFC_Ctrl_Vehicle_SocialInteraction_17

description: Library name: 22L005548

value: medial prefrontal cortex


title: DSP-1001660014603-D-B12

description: Library name: Sample 73


title: DSP-1001660014603-D-B11

description: Library name: Sample 72


title: AAV8 Control, replicate 2

description: Library name: siControl-2

value: WT


title: AAV8 Control, replicate 1

description: Library name: siControl-1


title: DSP-1001660014603-D-H11

description: Library name: Sample 144


title: PFC_Ctrl_Vehicle_SocialInteraction_89

description: Library name: 22L005544


city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: Dam-LMNB1-Forelimbs_Plate217_mpimg_L25684_RPI18
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

data_processing:
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq R2 reads are aligned using GRCm38 (v. 89) transcript models and hisat2 (v. 2.1.0) with the following paramters: : “--mp 2,0 --sp 4,0”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Assembly: mm10
Supplementary files format and content: RNA count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; DamID count table: count table containing UMI-unique GATC counts per 20-kb interval for all single-cell samples; sample annotations: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. DamID and CELseq barcodes follow a 3-NNNN-3-NNNN format, where "N" positions indicate the barcode-specific sequence,  the "3" indicates positions of a 3nt UMI sequence.

source_name: Forelimbs

growth_protocol: scDam&T data collection was performed in transgenic C2 ESCs and mice carrying an inducible Dam-LMNB1 transgene. For mice, Dam-LMNB1 animals were bred with CAG-CreER mice to facilitate induction and, for mutant analyses, also with Sox9-Kcnj2 ΔCTCF mice. All mouse lines were maintained in a C57Bl.6/J background. For ESCs, a CreERT2 coding sequence was incorporated into the Dam-LMNB1 transgene to facilitate induction. Mouse G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid) or C2 ESCs (Cellosurus) were grown as described previously on a mitomycin-inactivated CD1 mouse embryonic fibroblast feeder monolayer on gelatinised dishes at 37°C, 7.5% CO2. All ESCs were cultured in ESC medium containing knockout DMEM with 4,5 mg/ml glucose and sodium pyruvate supplemented with 15% FCS , 10 mM Glutamine, 1x penicillin/streptomycin , 1x non-essential amino acids, 1x nucleosides, 0.1 mM beta-Mercaptoethanol and 1000 U/ml LIF.

extract_protocol:
Embryos were isolated from the uteri of pregnant mothers between 8.5 and 13.5 days after the plug date. Embryos were dissected on ice in HBBS (for 8.5-day embryos) or PBS (for 9.5-13.5-day embryos), and staged based on morphology, size, and/or somite number.Samples were processed to create single cell suspensions differently depending on stage. Whole E8.5 embryos were pooled by precise somite number and transferred for tissue dissociation in 200 μl TrypLE Express (Gibco,12604013; Gibco) at 37 °C and triturated by pipetting at 10-20 minutes intervals for a total of 40 minutes. By contrast, tissues from E9.5 to E13.5 embryos were microdissected and pooled as needed. Tissues were then dissociated with Trypsin-EDTA (Thermo Fisher, 25300096; Thermo Fisher) and trituration by pipetting at 37°C at 2-3 minute intervals until no visible clumps remained (~5-15 minutes). Digestion was immediately halted by addition of 10% FCS/PBS. Following disassociation, all samples were cleared of  cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware) and then pelleted by centrifugation at 300 g for 5 minutes at 4°C. Cells were resuspended in FACS buffer [10%FCS/PBS, 10μM ROCK inhibitor (M1817; AbMole), 1μg/ml DAPI (D9542; Sigma-Aldrich)] in preparation for single-cell sorting.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Tamoxifen injection was used to trigger Dam-LMNB1 expression in mice via Cre-ERT2 mediated recombination. For ESCs induction, 1 uM of 4-OHT (Sigma, SML1666) was added to the media 7 hours prior to harvesting the cells.

tag: technique

value: scDam&T-seq

value: Forelimbs

tag: Stage

value: tamoxifen induction

tag: plate

tag: subtypes

value: genomic DNA; mRNA


description:
Library name: Dam-LMNB1-Forelimbs_Plate216_mpimg_L25684_RPI16
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

tag: tissue


title: DSP-1001660014603-D-B10

description: Library name: Sample 71

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

tag: treatment

value: CONTROL


title: DSP-1001660014603-D-B09

description: Library name: Sample 70

tag: panel (wta_+ipa)


description:
Library name: Dam-LMNB1-Forelimbs_Plate215_mpimg_L25684_RPI15
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-B08

description: Library name: Sample 69

tag: scan name


title: DSP-1001660014603-D-B07

description: Library name: Sample 68

tag: roi


description:
Library name: Dam-LMNB1-Forelimbs_Plate212_mpimg_L25684_RPI14
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-B06

description: Library name: Sample 67

tag: segment


description:
Library name: Dam-LMNB1-Forelimbs_Plate211_mpimg_L25684_RPI13
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-B05

description: Library name: Sample 66


title: DSP-1001660014603-D-B04

description: Library name: Sample 65


description:
Library name: Dam-LMNB1-Hindlimbs_Plate179_mpimg_L25079_RPI7
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Hindlimb

value: Hindlimb


title: DSP-1001660014603-D-B03

description: Library name: Sample 64

value: DESMIN


description:
Library name: Dam-LMNB1-Forelimbs_Plate210_mpimg_L25684_RPI12
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Hindlimbs_Plate180_mpimg_L25079_RPI8
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Hindlimbs_Plate178_mpimg_L24603_RPI4
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-B02

description: Library name: Sample 63


title: DSP-1001660014603-D-B01

description: Library name: Sample 62


title: DSP-1001660014603-D-A12

description: Library name: Sample 61


description:
Library name: Dam-LMNB1-Hindlimbs_Plate166_mpimg_L24603_RPI2
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: SedIR_1 single-cell RNA-seq library

description: Library name: liver_SedIR_rep1

value: CD45+ immune cells

value: wild-type (WT C57BL/6)

value: ischemia-reperfusion injury (60min ischemia/6h reperfusion)


description:
Library name: Dam-LMNB1-Hindlimbs_Plate164_mpimg_L24603_RPI1
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-A11

description: Library name: Sample 60


title: DSP-1001660014603-D-A10

description: Library name: Sample 59


title: DSP-1001660014603-D-A09

description: Library name: Sample 58


description:
Library name: Dam-LMNB1-Forelimb_Plate143_mpimg_L23112_RPI38
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Forelimb

value: Forelimb


description:
Library name: Dam-LMNB1-Lung_Plate108_mpimg_L23112_RPI35
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Lung

value: Lung


description:
Library name: Dam-LMNB1-Intestine_Plate118_mpimg_L23112_RPI36
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Intestine

value: Intestine


title: DSP-1001660014603-D-A08

description: Library name: Sample 57


description:
Library name: Dam-LMNB1-Kidney_Plate103_mpimg_L23112_RPI32
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Kidney

value: Kidney


title: DSP-1001660014603-D-A07

description: Library name: Sample 56


title: DSP-1001660014603-D-A06

description: Library name: Sample 55


description:
Library name: Dam-LMNB1-Forelimb_Plate10_mpimg_L23112_RPI27
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Forelimb_Plate141_mpimg_L23112_RPI20
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-A05

description: Library name: Sample 54


description:
Library name: Dam-LMNB1-Whole_embryo_Plate90_mpimg_L23112_RPI19
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-A04

description: Library name: Sample 53


description:
Library name: Dam-LMNB1-Whole_embryo_Plate89_mpimg_L23112_RPI14
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-A03

description: Library name: Sample 52


description:
Library name: Dam-LMNB1-ESCs_Plate83_mpimg_L23112_RPI11
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: ESCs

value: ESCs


description:
Library name: Dam-LMNB1-Forelimb_Plate142_mpimg_L23112_RPI37
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Midbrain_Plate117_mpimg_L23112_RPI33
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Midbrain

value: Midbrain


title: DSP-1001660014456-E-E03

description: Library name: Sample 50

value: CF

value: Desmin


title: DSP-1001660014456-E-E02

description: Library name: Sample 49


description:
Library name: Dam-LMNB1-Gonad_F_Plate109_mpimg_L23112_RPI31
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: scDam&T-seq

value: tamoxifen induction


title: DSP-1001660014456-E-E01

description: Library name: Sample 48

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


description:
Library name: Dam-LMNB1-Gonad_F_Plate100_mpimg_L23112_RPI28
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: genomic DNA; mRNA


title: DSP-1001660014456-E-D12

description: Library name: Sample 47


description:
Library name: Dam-LMNB1-Forelimb_Plate131_mpimg_L23112_RPI25
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: KO3

description: Library name: SV9-KO3

value: Cortex

value: Cortical projection neurons

value: NexCre/+;Cdk7lox/lox, R26EYFP/+


description:
Library name: Dam-LMNB1-Forelimb_Plate122_mpimg_L23112_RPI23
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-D11

description: Library name: Sample 46


title: DSP-1001660014456-E-D10

description: Library name: Sample 45


description:
Library name: Dam-LMNB1-Hindlimbs_Plate9_mpimg_L23112_RPI16
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Hindlimb


title: DSP-1001660014456-E-D09

description: Library name: Sample 44


title: DSP-1001660014456-E-D08

description: Library name: Sample 43


description:
Library name: Dam-LMNB1-Forelimb_Plate121_mpimg_L23112_RPI22
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Forelimb_Plate128_mpimg_L23112_RPI8
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-D07

description: Library name: Sample 42


description:
Library name: Dam-LMNB1-Forelimb_Plate127_mpimg_L23112_RPI7
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-D06

description: Library name: Sample 41


description:
Library name: Dam-LMNB1-Hindlimbs_Plate126_mpimg_L23112_RPI4
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-D05

description: Library name: Sample 40


title: DSP-1001660014456-E-D04

description: Library name: Sample 39

value: PF


description:
Library name: Dam-LMNB1-Intestine_Plate115_mpimg_L23112_RPI48
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-D03

description: Library name: Sample 38


description:
Library name: Dam-LMNB1-Kidney_Plate102_mpimg_L23112_RPI47
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Forelimb_Plate84_mpimg_L23112_RPI3
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Forelimb


title: DSP-1001660014456-E-D02

description: Library name: Sample 37


title: DSP-1001660014456-E-D01

description: Library name: Sample 36


description:
Library name: Dam-LMNB1-Gonad_M_Plate101_mpimg_L23112_RPI46
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Forelimb_Plate99_mpimg_L23112_RPI45
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-C12

description: Library name: Sample 35


description:
Library name: Dam-LMNB1-Midbrain_Plate114_mpimg_L23112_RPI44
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-C11

description: Library name: Sample 34


description:
Library name: Dam-LMNB1-Forebrain_Plate113_mpimg_L23112_RPI43
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Forebrain

value: Forebrain


title: DSP-1001660014456-E-C10

description: Library name: Sample 33


description:
Library name: Dam-LMNB1-Heart_Plate105_mpimg_L23112_RPI40
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Heart

value: Heart


title: DSP-1001660014456-E-C08

description: Library name: Sample 31


description:
Library name: Dam-LMNB1-Whole_embryo_Plate49_mpimg_L22453_RPI39
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-C09

description: Library name: Sample 32


description:
Library name: Dam-LMNB1-Hindlimb_Plate112_mpimg_L23112_RPI42
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-C07

description: Library name: Sample 30


description:
Library name: Dam-LMNB1-Forebrain_Plate43_mpimg_L22453_RPI38
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: scMultiome_WT_GEX

description:
Library name: WT_GEX
10X Genomics

value: Spleen

value: P14 CD8+ primary T cells

value: LCMV CL13 infection


title: DSP-1001660014456-E-C06

description: Library name: Sample 29


description:
Library name: Dam-LMNB1-Forelimb_Plate26_mpimg_L22453_RPI36
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Whole_embryo_Plate47_mpimg_L22453_RPI35
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-C04

description: Library name: Sample 27

value: IA


description:
Library name: Dam-LMNB1-Midbrain_Plate46_mpimg_L22453_RPI34
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Midbrain


title: DSP-1001660014456-E-C05

description: Library name: Sample 28


title: DSP-1001660014456-E-C03

description: Library name: Sample 26


description:
Library name: Dam-LMNB1-Forelimb_Plate22_mpimg_L22453_RPI32
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: scDam&T-seq


title: DSP-1001660014456-E-C02

description: Library name: Sample 25


description:
Library name: Dam-LMNB1-Intestine_Plate33_mpimg_L22453_RPI33
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Intestine

value: tamoxifen induction


title: DSP-1001660014456-E-B12

description: Library name: Sample 23

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: DSP-1001660014456-E-C01

description: Library name: Sample 24


description:
Library name: Dam-LMNB1-Lung_Plate45_mpimg_L22453_RPI28
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Lung

value: genomic DNA; mRNA


title: DSP-1001660014456-E-B11

description: Library name: Sample 22


description:
Library name: Dam-LMNB1-Whole_embryo_Plate48_mpimg_L22453_RPI30
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


description:
Library name: Dam-LMNB1-Hindlimbs_Plate15_mpimg_L22453_RPI27
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-B10

description: Library name: Sample 21

value: Desmin


description:
Library name: Dam-LMNB1-ESCs_Plate81_mpimg_L22453_RPI25
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: ESCs


title: DSP-1001660014456-E-B09

description: Library name: Sample 20

value: PF


description:
Library name: Dam-LMNB1-Lung_Plate39_mpimg_L22453_RPI22
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014603-D-A02

description: Library name: Sample 51

value: CONTROL


title: DSP-1001660014456-E-B07

description: Library name: Sample 18


title: DSP-1001660014456-E-B08

description: Library name: Sample 19


description:
Library name: Dam-LMNB1-Hindlimbs_Plate37_mpimg_L22453_RPI21
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Hindlimb


description:
Library name: Dam-LMNB1-Forelimb_Plate35_mpimg_L22453_RPI20
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

value: Forelimb


description:
Library name: Dam-LMNB1-Forelimb_Plate20_mpimg_L22453_RPI19
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-B05

description: Library name: Sample 16

value: CF


title: DSP-1001660014456-E-B06

description: Library name: Sample 17


description:
Library name: Dam-LMNB1-Hindlimbs_Plate19_mpimg_L22453_RPI18
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-B04

description: Library name: Sample 15


description:
Library name: Dam-LMNB1-Limb_Plate1_mpimg_L22453_RPI16
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file

source_name: Limb

value: Limb


title: DSP-1001660014456-E-B03

description: Library name: Sample 14


description:
Library name: Dam-LMNB1-Forelimb_Plate40_mpimg_L22453_RPI15
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-B02

description: Library name: Sample 13


description:
Library name: Dam-LMNB1-Hindlimbs_Plate36_mpimg_L22453_RPI14
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-B01

description: Library name: Sample 12


title: DSP-1001660014456-E-A12

description: Library name: Sample 11


description:
Library name: Dam-LMNB1-Forelimb_Plate11_mpimg_L22453_RPI12
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: DSP-1001660014456-E-A11

description: Library name: Sample 10


title: DSP-1001660014456-E-A10

description: Library name: Sample 9


description:
Library name: Dam-LMNB1-Forelimb_Plate16_mpimg_L22453_RPI13
scDamT-seq provides both a genomic and a transcriptomic read-out in the same fastq file


title: mpimg_L26647-1_RNA-Limbs

description:
Library name: mpimg_L26647-1_RNA-Limbs
files with prefix "reseq" result from the resequencing of the same samples to obtain more reads

data_processing:
Counts for the open chromatin and transcriptional read-outs were obtained by running the cellranger-arc count pipeline with default settings.
Assembly: mm10
Supplementary files format and content: cellranger output files: atac_fragments.tsv.gz (ATAC) and filtered_feature_bc_matrix.h5 (RNA); sample annotations: table containing detailed sample information for all single-cell samples

source_name: ESCs and Limb

growth_protocol: 10x multiome data collection was performed using C57Bl.6/J mice that were sourced from Inotiv and G4 ESCs (XY, 129S6/SvEvTac x C57BL/6Ncr F1 hybrid)

extract_protocol:
Embryos were isolated from the uteri of pregnant mothers between 8.5 and 13.5 days after the plug date. Embryos were dissected on ice in HBBS (for 8.5-day embryos) or PBS (for 9.5-13.5-day embryos), and staged based on morphology, size, and/or somite number.Samples were processed to create single cell suspensions differently depending on stage. Whole E8.5 embryos were pooled by precise somite number and transferred for tissue dissociation in 200 μl TrypLE Express (Gibco,12604013; Gibco) at 37 °C and triturated by pipetting at 10-20 minutes intervals for a total of 40 minutes. By contrast, tissues from E9.5 to E13.5 embryos were microdissected and pooled as needed. Tissues were then dissociated with Trypsin-EDTA (Thermo Fisher, 25300096; Thermo Fisher) and trituration by pipetting at 37°C at 2-3 minute intervals until no visible clumps remained (~5-15 minutes). Digestion was immediately halted by addition of 10% FCS/PBS. Following disassociation, all samples were cleared of  cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware) and then pelleted by centrifugation at 300 g for 5 minutes at 4°C. Cells were resuspended in 1:1 ratio of F1 [40% FCS/60% DMEM] and F2 solution [20%DMSO/40%FCS/40% DMEM] and cryopreserved.
Cryopreserved single-cell suspensions were used to prepare nuclei according to 10x Genomics guidelines with few modifications. Briefly, cells were thawed at 37°C and immediately washed twice with warm ESC media by centrifugation at 400 g for 10 minutes at RT. Pipetting was performed as gently as possible to ensure cell viability. Cells were then transferred onto ice and washed twice with cold 0.04%BSA/PBS by centrifugation at 400 g for 10 minutes at 4°C. After the final wash, the pellet was thoroughly resuspended in lysis buffer diluent (lysis buffer without tween, NP-40, or digitonin) [10 mM Tris-HCl (pH 7.4) (Roth, 9090.3), 10 mM NaCl (Invitrogen, AM9760G), 3 mM MgCl₂ (Roth, 2189.1), 1% BSA (Sigma, 810531), 1 mM DTT (have to check), DEPC water] to generate single cell-suspension. An equal volume of 2x concentrated lysis buffer [20 mM Tris-HCl (pH 7.4), 20 mM NaCl, 6 mM MgCl₂ , 0.20% Tween-20 (Serva, 37470), 0.20% NP40 substitute (have to check), 0.02% Digitonin (Milipore, 30410), 2% BSA, 2 mM DTT, DEPC water]  was added to the cell suspension, mixed by inversion, left to incubate on ice for  3 (embryonic tissues) or 5 minutes (ESCs). Nuclei were then washed three times with Wash buffer by centrifugation at 500g for 5 minutes at 4°C. Prior to the last centrifugation, samples were cleared of cell clumps by filtration (40 μm, Flowmi Cell Strainer, Scienceware). Nuclei were resuspended in 10x Genomics diluted nucleus buffer (PN-2000207), quantified using a haemocytometer and adjusted to 3,220 nuclei per μl. In total, 5 μl of diluted nuclei were subsequently used for the transposase reaction. All steps were performed on a RNAse-Zap treated bench. All buffers were supplemented with 1 U/μl RNAse inhibitor (1:1 ratio of Invitrogen, AM2684 and AM2694; Invitrogen). The final libraries were sequenced on the Illumina NovaSeq 6000 or NovaSeq X Plus platform with paired-end 50/50bp, 28/90bp or 50/90bp read length.

value: ESCs and Limb

value: wt


title: mpimg_L26649-1_ATAC-Limbs

description:
Library name: mpimg_L26649-1_ATAC-Limbs
files with prefix "reseq" result from the resequencing of the same samples to obtain more reads


title: DSP-1001660014456-E-A09

description: Library name: Sample 8


title: DSP-1001660014456-E-A08

description: Library name: Sample 7


title: mpimg_L24607-1_RNA-E9-5

description: Library name: mpimg_L24607-1_RNA-E9-5


title: mpimg_L24605-1_ATAC-E9-5

description: Library name: mpimg_L24605-1_ATAC-E9-5


title: DSP-1001660014456-E-A07

description: Library name: Sample 6


title: DSP-1001660014456-E-A06

description: Library name: Sample 5


title: mpimg_L24606-1_RNA-E8-5

description: Library name: mpimg_L24606-1_RNA-E8-5

source_name: Whole embryo

value: Whole embryo


title: mpimg_L24604-1_ATAC-E8-5

description: Library name: mpimg_L24604-1_ATAC-E8-5


title: DSP-1001660014456-E-A05

description: Library name: Sample 4


title: snMuscle_TAM_Control_Rep1

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

data_processing:
Fastq files were processed using 10x Genomic's CellRanger Pipeline
barcode, matrix and feature files were imported into Seurat for downstream analysis and cell annotation.
Assembly: mm10
Supplementary files format and content: barcode, matrix and feature files contain the output from CellRanger.

source_name: muscle

extract_protocol:
nuclei were extracted using a a dounce homogenizer as in Grandi 2022 Nature Protocols
Libraries were made following the 10x 3' Gex manual with no modifications. 11 PCR cycles were performed.

value: muscle

tag: Sex

value: female

tag: age

value: 20 weeks

value: WT Control

tag: muscle type

value: tibialis anterior


title: DSP-1001660014456-E-A02

description: Library name: Sample 1

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein


title: snMuscle_TAM_Control_Rep2


title: snMuscle_TAM_MBLKD_Rep2

value: MBnl1 KD


title: DSP-1001660014456-E-A03

description: Library name: Sample 2


title: DSP-1001660014456-E-A04

description: Library name: Sample 3

value: Desmin


title: DSP-1001660019865-Z-F02

description: Library name: Sample 301

library_source: other

data_processing:
/opt/illumina/Isas/1.37.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R  /data/scratch/workspace/RunFolder --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
raw sequencing data  were processed using Illumina basespace pipeline to generate fastq files
Run Nanostring GeoMx NGS pipeline ( version 3.1.1.6)  to generate DCC files
Upload DCC files to GeoMx DSP platform and create the study
Perfom standand QC using default parameters setting recommended by the manufacture
Q3 normalization was carried out to generate Q3 normalization datasets  which are for the all downstream analysis
Assembly: GRCh38
Supplementary files format and content: raw_dcc.tar:  raw read counts in DCC of tar
Supplementary files format and content: Protein_Q3_normalized_expression_matrix.txt  :  normalization gene expression matrix by Q3 normalization recommended by manufacture which are used for all the downstream analysis in txt format

molecule: protein

value: PF


title: snMuscle_TAM_MBLKD_Rep1


title: SNI_rep2_8

type: RNA

city: Boston

first: Yi

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

description: MERFISH

hyb_protocol: The samples on the coverslips were thawed for 5 min at room temperature, fixed with 4% PFA for 10 min and washed twice with 1× PBS. The samples were stored in 70% ethanol at 4 °C for 24 h to permeabilize the cells. Next, the samples were washed twice with 2× SSC and once with encoding probe wash buffer (30% formamide in 2× SSC) for 5 min. Then the coverslip was inverted onto a 50 μl encoding probe buffer droplet on the flat parafilm in a petri dish. The encoding probe buffer contained a total of 3 μM encoding probes, 2 μM polyA-anchor probes, 30% formamide, 0.1% yeast tRNA, 10% dextran sulfate and 2× SSC. The coverslip was incubated at 37 °C for 36 h in a small humidified box in an incubator. Next, the coverslips was washed twice with the encoding probe wash buffer at 47 °C for 30 min. Then the samples were embedded in a thin polyacrylamide gel by inverting the coverslip onto a 65 μl gel solution on a gel-slick coated glass slides and incubated at room temperature for 2 h to allow the gel to polymerize. The gel embedded coverslip was carefully peeled up, put into the digestion buffer (2× SSC, 2% SDS, 0.25% Triton X-100, 1% proteinase K) and incubated at 37 °C for 48 h. After digestion, the coverslip was washed with 2× SSC at room temperature for 30 min on a rocking platform, and this wash was repeated four times.

scan_protocol: The imaging system for MERFISH was customized built. The fluidics system was automatically controlled by the open-source software (https://github.com/ZhuangLab/storm-control). All the buffers used in the fluidics system were made according to the protocols described in Cadinu et al. and degassed for 10 min under vacuum prior to use. The software coordinating both the imaging system and the fluidics system to automatically perform MERFISH data acquisition was customized developed. We used the Nikon CFI Plan Apochromat Lambda D 10X objective to define the imaging regions (field of view, FOV). The Nikon CFI Plan Apochromat Lambda D 60X Oil objective was used for MERFISH imaging. The multiple rounds of readout probe hybridization, imaging and fluorescence cleavage process were executed for a total of 12 rounds for the 24-bit barcodes. For each FOV, we imaged 7 z-stack planes with a step of 1.5 μm. The 405 channel was used to image the DAPI and the 477 channel was used to image the total polyA RNA signals only in the first round of imaging, both of which were used for cell segmentation. The 545 channel was used to image the beads (Invitrogen, F8800) coated onto the coverslip, which was used to align the images across different rounds of imaging. The 748 and 637 channel were used for the readouts imaging of the two bits in the barcodes per imaging round.

data_processing: The raw imaging data of MERFISH were decoded using the MERlin (https://github.com/emanuega/MERlin) pipeline with customized modification to adapt to our custom-built machine. We employed the Cellpose software for cell segmentation based on the DAPI and total polyA RNA signals. The decoding results including the cell-by-gene count matrix, cell centroid coordinates and cell boundaries were loaded into the R package Seurat (v5.3.0) for downstream analysis. We only kept the cells with at least 60 RNAs and at least 20 different genes detected in the cell.    The raw counts were normalized using SCTransform. The PCAs were calculated with the RunPCA function and the UMAPs were generated with the RunUMAP function. The single cells were clustered using FindNeighbors and FindClusters with a resolution of 4. The cell type of each cell was first automatically annotated with reference mapping using the FindTransferAnchors and TransferData functions, leveraging the above described public scRNA-seq data of insula cortex from the Allen Brain Map as the reference. For the cells in one cluster, the most frequent cell type annotated from the reference mapping was used as the cell type for this cluster of cells. Then the cell type annotation for each cluster was manually checked and adjusted based on the marker genes of each cluster.

molecule: cytoplasmic RNA

source_name: SNI

extract_protocol: The fresh frozen samples in OCT were sectioned into 10 μm slices in a cryostat (Leica, CM3050) prechilled to -20 °C and mounted onto the treated coverslips.

tag: gender

value: male

value: brain insula cortex 10μm slice


title: DSP-1001660019865-Z-F01

description: Library name: Sample 300


title: SNI_rep2_7

description: MERFISH


title: SNI_rep2_6

description: MERFISH


title: DSP-1001660019865-Z-E12

description: Library name: Sample 299


title: DSP-1001660019865-Z-E11

description: Library name: Sample 298


title: SNI_rep2_5

description: MERFISH


title: SNI_rep2_3

description: MERFISH


title: SNI_rep2_4

description: MERFISH


title: DSP-1001660019865-Z-E09

description: Library name: Sample 296


title: DSP-1001660019865-Z-E08

description: Library name: Sample 295


title: SNI_rep2_2

description: MERFISH


title: SNI_rep2_1

description: MERFISH


title: DSP-1001660019865-Z-E10

description: Library name: Sample 297


title: DSP-1001660019865-Z-E06

description: Library name: Sample 293


title: DSP-1001660019865-Z-E07

description: Library name: Sample 294


title: SNI_rep1_8

description: MERFISH


title: DSP-1001660019865-Z-E05

description: Library name: Sample 292


title: DSP-1001660019865-Z-E04

description: Library name: Sample 291


title: SNI_rep1_7

description: MERFISH


title: DSP-1001660019865-Z-E03

description: Library name: Sample 290


title: SNI_rep1_6

description: MERFISH


title: SNI_rep1_4

description: MERFISH


title: DSP-1001660019865-Z-E01

description: Library name: Sample 288


title: SNI_rep1_5

description: MERFISH


title: SNI_rep1_3

description: MERFISH


title: DSP-1001660019865-Z-E02

description: Library name: Sample 289


title: SNI_rep1_2

description: MERFISH


title: DSP-1001660019865-Z-D12

description: Library name: Sample 287


title: DSP-1001660019865-Z-D11

description: Library name: Sample 286


title: SNI_rep1_1

description: MERFISH


title: DSP-1001660019865-Z-D10

description: Library name: Sample 285


title: Sham_rep2_8

description: MERFISH

source_name: Sham


title: Sham_rep2_7

description: MERFISH


title: Sham_rep2_5

description: MERFISH


title: DSP-1001660019865-Z-D07

description: Library name: Sample 282


title: Sham_rep2_6

description: MERFISH


title: DSP-1001660019865-Z-D09

description: Library name: Sample 284


title: DSP-1001660019865-Z-D08

description: Library name: Sample 283


title: DSP-1001660019865-Z-D05

description: Library name: Sample 280


title: DSP-1001660019865-Z-D06

description: Library name: Sample 281


title: Sham_rep2_4

description: MERFISH


title: Sham_rep2_3

description: MERFISH


title: DSP-1001660019865-Z-D03

description: Library name: Sample 278


title: DSP-1001660019865-Z-D04

description: Library name: Sample 279


title: Sham_rep2_2

description: MERFISH


title: Sham_rep2_1

description: MERFISH


title: DSP-1001660019865-Z-D02

description: Library name: Sample 277


title: Sham_rep1_8

description: MERFISH


title: DSP-1001660019865-Z-D01

description: Library name: Sample 276


title: DSP-1001660019865-Z-C12

description: Library name: Sample 275


title: Sham_rep1_6

description: MERFISH


title: Sham_rep1_7

description: MERFISH


title: DSP-1001660019865-Z-C11

description: Library name: Sample 274


title: Sham_rep1_5

description: MERFISH


title: DSP-1001660019865-Z-C10

description: Library name: Sample 273


title: DSP-1001660019865-Z-C09

description: Library name: Sample 272


title: DSP-1001660019865-Z-C08

description: Library name: Sample 271


title: Sham_rep1_4

description: MERFISH


title: Sham_rep1_2

description: MERFISH


title: Sham_rep1_3

description: MERFISH


title: DSP-1001660019865-Z-C07

description: Library name: Sample 270


title: Sham_rep1_1

description: MERFISH


title: DSP-1001660019865-Z-C06

description: Library name: Sample 269


title: CTB_mouse7_7

description: MERFISH

source_name: CTB748: HYT CTB637: BLA


title: CTB_mouse7_8

description: MERFISH


title: DSP-1001660019865-Z-C04

description: Library name: Sample 267


title: CTB_mouse7_5

description: MERFISH


title: DSP-1001660019865-Z-C03

description: Library name: Sample 266


title: CTB_mouse7_4

description: MERFISH


title: DSP-1001660019865-Z-C05

description: Library name: Sample 268


title: DSP-1001660019865-Z-C02

description: Library name: Sample 265


title: DSP-1001660019865-Z-C01

description: Library name: Sample 264


title: CTB_mouse7_6

description: MERFISH


title: CTB_mouse7_3

description: MERFISH


title: CTB_mouse7_2

description: MERFISH


title: DSP-1001660019865-Z-B12

description: Library name: Sample 263


title: DSP-1001660019865-Z-B11

description: Library name: Sample 262


title: CTB_mouse7_1

description: MERFISH


title: CTB_mouse6_8

description: MERFISH

source_name: CTB748: mPFC CTB637: SSp


title: DSP-1001660019865-Z-B10

description: Library name: Sample 261


title: DSP-1001660019865-Z-B08

description: Library name: Sample 259


title: CTB_mouse6_6

description: MERFISH


title: DSP-1001660019865-Z-B07

description: Library name: Sample 258


title: DSP-1001660019865-Z-B09

description: Library name: Sample 260


title: CTB_mouse6_7

description: MERFISH


title: CTB_mouse6_4

description: MERFISH


title: CTB_mouse6_5

description: MERFISH


title: DSP-1001660019865-Z-B05

description: Library name: Sample 256

value: IA


title: DSP-1001660019865-Z-B06

description: Library name: Sample 257

value: CF


title: CTB_mouse6_3

description: MERFISH


title: DSP-1001660019865-Z-B04

description: Library name: Sample 255


title: CTB_mouse6_2

description: MERFISH


title: DSP-1001660019865-Z-B03

description: Library name: Sample 254


title: CTB_mouse6_1

description: MERFISH


title: DSP-1001660019865-Z-B02

description: Library name: Sample 253


title: CTB_mouse5_8

description: MERFISH

source_name: CTB748: CPu CTB637: NAc


title: DSP-1001660019865-Z-B01

description: Library name: Sample 252


title: DSP-1001660019865-Z-A12

description: Library name: Sample 251


title: CTB_mouse5_6

description: MERFISH


title: CTB_mouse5_7

description: MERFISH


title: DSP-1001660019865-Z-A11

description: Library name: Sample 250


title: CTB_mouse5_5

description: MERFISH


title: DSP-1001660019865-Z-A10

description: Library name: Sample 249


title: DSP-1001660019865-Z-A09

description: Library name: Sample 248


title: CTB_mouse5_4

description: MERFISH


title: CTB_mouse5_3

description: MERFISH


title: DSP-1001660019865-Z-A08

description: Library name: Sample 247


title: CTB_mouse5_2

description: MERFISH


title: DSP-1001660019865-Z-A07

description: Library name: Sample 246


title: DSP-1001660019865-Z-A06

description: Library name: Sample 245


title: CTB_mouse4_8

description: MERFISH

source_name: CTB748: pcIC CTB637: NTS


title: DSP-1001660019865-Z-A05

description: Library name: Sample 244


title: CTB_mouse4_6

description: MERFISH


title: CTB_mouse4_7

description: MERFISH


title: DSP-1001660019865-Z-A04

description: Library name: Sample 243


title: CTB_mouse5_1

description: MERFISH


title: DSP-1001660019865-Z-A03

description: Library name: Sample 242


title: CTB_mouse4_5

description: MERFISH


title: DSP-1001660019865-Z-A02

description: Library name: Sample 241


title: DSP-1001660014867-Y-H12

description: Library name: Sample 240


title: CTB_mouse4_4

description: MERFISH


title: CTB_mouse4_3

description: MERFISH


title: DSP-1001660014867-Y-H11

description: Library name: Sample 239


title: DSP-1001660014867-Y-H10

description: Library name: Sample 238


title: CTB_mouse4_2

description: MERFISH


title: CTB_mouse4_1

description: MERFISH


title: DSP-1001660014867-Y-H09

description: Library name: Sample 237


title: DSP-1001660014867-Y-H08

description: Library name: Sample 236


title: DSP-1001660014867-Y-H07

description: Library name: Sample 235


title: CTB_mouse3_7

description: MERFISH

source_name: CTB748: PAG CTB637: PBN


title: CTB_mouse3_8

description: MERFISH


title: CTB_mouse3_6

description: MERFISH


title: CTB_mouse3_5

description: MERFISH


title: DSP-1001660014867-Y-H06

description: Library name: Sample 234


title: DSP-1001660014867-Y-H05

description: Library name: Sample 233


title: CTB_mouse3_4

description: MERFISH


title: DSP-1001660014867-Y-H04

description: Library name: Sample 232


title: DSP-1001660014867-Y-H03

description: Library name: Sample 231


title: CTB_mouse3_2

description: MERFISH


title: DSP-1001660014867-Y-H02

description: Library name: Sample 230


title: CTB_mouse3_1

description: MERFISH


title: DSP-1001660014867-Y-H01

description: Library name: Sample 229


title: DSP-1001660014867-Y-G12

description: Library name: Sample 228


title: CTB_mouse2_8

description: MERFISH

source_name: CTB748: MRN CTB637: CeA


title: CTB_mouse2_7

description: MERFISH


title: DSP-1001660014867-Y-G11

description: Library name: Sample 227


title: CTB_mouse2_6

description: MERFISH


title: DSP-1001660014867-Y-G10

description: Library name: Sample 226


title: DSP-1001660014867-Y-G09

description: Library name: Sample 225


title: CTB_mouse2_5

description: MERFISH


title: CTB_mouse2_3

description: MERFISH


title: DSP-1001660014867-Y-G08

description: Library name: Sample 224


title: CTB_mouse2_2

description: MERFISH


title: DSP-1001660014867-Y-G06

description: Library name: Sample 222


title: CTB_mouse1_8

description: MERFISH

source_name: CTB748: TH CTB637: acIC


title: DSP-1001660014867-Y-G07

description: Library name: Sample 223


title: DSP-1001660014867-Y-G04

description: Library name: Sample 220


title: CTB_mouse1_7

description: MERFISH


title: DSP-1001660014867-Y-G03

description: Library name: Sample 219


title: CTB_mouse2_1

description: MERFISH


title: DSP-1001660014867-Y-G05

description: Library name: Sample 221


title: CTB_mouse1_6

description: MERFISH


title: DSP-1001660014867-Y-G02

description: Library name: Sample 218


title: DSP-1001660014867-Y-G01

description: Library name: Sample 217


title: CTB_mouse1_5

description: MERFISH


title: CTB_mouse1_4

description: MERFISH


title: DSP-1001660014867-Y-F12

description: Library name: Sample 216


title: DSP-1001660014867-Y-F11

description: Library name: Sample 215


title: CTB_mouse1_3

description: MERFISH


title: CTB_mouse1_2

description: MERFISH


title: CTB_mouse1_1

description: MERFISH


title: DSP-1001660014867-Y-F09

description: Library name: Sample 213


title: DSP-1001660014867-Y-F08

description: Library name: Sample 212


title: WT_female_rep1_8

description: MERFISH

source_name: WT


title: DSP-1001660014867-Y-F10

description: Library name: Sample 214


title: WT_female_rep1_7

description: MERFISH


title: DSP-1001660014867-Y-F07

description: Library name: Sample 211


title: WT_female_rep1_6

description: MERFISH


title: DSP-1001660014867-Y-F06

description: Library name: Sample 210


title: WT_female_rep1_5

description: MERFISH


title: WT_female_rep1_4

description: MERFISH


title: DSP-1001660014867-Y-F03

description: Library name: Sample 207


title: DSP-1001660014867-Y-F04

description: Library name: Sample 208


title: WT_female_rep1_3

description: MERFISH


title: DSP-1001660014867-Y-F02

description: Library name: Sample 206


title: WT_female_rep1_2

description: MERFISH


title: DSP-1001660014867-Y-F05

description: Library name: Sample 209


title: WT_female_rep1_1

description: MERFISH


title: DSP-1001660014867-Y-F01

description: Library name: Sample 205


title: DSP-1001660014867-Y-E12

description: Library name: Sample 204


title: WT_male_rep2_8

description: MERFISH


title: WT_male_rep2_7

description: MERFISH


title: DSP-1001660014867-Y-E11

description: Library name: Sample 203


title: WT_male_rep2_6

description: MERFISH


title: WT_male_rep2_4

description: MERFISH


title: DSP-1001660014867-Y-E09

description: Library name: Sample 201


title: WT_male_rep2_5

description: MERFISH


title: WT_male_rep2_3

description: MERFISH


title: DSP-1001660014867-Y-E07

description: Library name: Sample 199


title: DSP-1001660014867-Y-E10

description: Library name: Sample 202


title: DSP-1001660014867-Y-E08

description: Library name: Sample 200


title: WT_male_rep2_2

description: MERFISH


title: CTB_mouse3_3

description: MERFISH


title: WT_male_rep2_1

description: MERFISH


title: DSP-1001660014867-Y-E06

description: Library name: Sample 198


title: DSP-1001660014867-Y-E05

description: Library name: Sample 197


title: WT_male_rep1_16

description: MERFISH


title: CTB_mouse2_4

description: MERFISH


title: DSP-1001660014867-Y-E04

description: Library name: Sample 196


title: WT_male_rep1_14

description: MERFISH


title: DSP-1001660014867-Y-E03

description: Library name: Sample 195


title: WT_male_rep1_13

description: MERFISH


title: WT_male_rep1_12

description: MERFISH


title: DSP-1001660014867-Y-E02

description: Library name: Sample 194


title: WT_male_rep1_15

description: MERFISH


title: DSP-1001660014867-Y-E01

description: Library name: Sample 193


title: DSP-1001660014867-Y-D12

description: Library name: Sample 192


title: WT_male_rep1_11

description: MERFISH


title: DSP-1001660014867-Y-D11

description: Library name: Sample 191


title: WT_male_rep1_10

description: MERFISH


title: WT_male_rep1_9

description: MERFISH


title: DSP-1001660014867-Y-D10

description: Library name: Sample 190


title: WT_male_rep1_8

description: MERFISH


title: DSP-1001660014867-Y-D09

description: Library name: Sample 189


title: DSP-1001660014867-Y-D08

description: Library name: Sample 188


title: WT_male_rep1_7

description: MERFISH


title: DSP-1001660014867-Y-D06

description: Library name: Sample 186


title: DSP-1001660014867-Y-D07

description: Library name: Sample 187


title: WT_male_rep1_6

description: MERFISH


title: DSP-1001660014867-Y-D05

description: Library name: Sample 185


title: WT_male_rep1_5

description: MERFISH


title: WT_male_rep1_4

description: MERFISH


title: DSP-1001660014867-Y-D03

description: Library name: Sample 183


title: DSP-1001660014867-Y-D04

description: Library name: Sample 184


title: WT_male_rep1_3

description: MERFISH


title: DSP-1001660014867-Y-D02

description: Library name: Sample 182


title: WT_male_rep1_2

description: MERFISH


title: DSP-1001660014867-Y-D01

description: Library name: Sample 181


title: WT_male_rep1_1

description: MERFISH


title: Mild preeclampsia 004 T145

city: Bangkok

first: Natthaya

last: Chuaypen

state: Select a State or Province

address: 1873 Rama 4 road, Pathumwan

country: Thailand

institute: Chulalongkorn University, Faculty of Medicine

description: microRNA Expression

data_processing: All statistical analyses were calculated with SPSS Version 22 (SPSS, Chicago, IL) and GraphPad Prism 8 (GraphPad Software Inc., California, USA). The NanoString analysis was performed using nSolver Analysis Software (Version 4.0)

source_name: Mild preeclampsia

extract_protocol:
A total of 12 serum were collected from pregnant women . RNA extraction from serum samples (200 µl) were used for total RNA extraction using the miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s instruction
A total of 12 serum were randomly selected from the stored samples to investigate the expression profile of 800 human miRNAs using the nCounter® Human v3 miRNA Expression Assays (NanoString Technologies, Seattle, USA)
Serum was collected from 20 severe preeclampsia pregnancies, 20 mild preeclampsia pregnancies and 20 healthy pregnancies after fasting by centrifugation under sterile conditions. Serum samples (200 µl) were used for total RNA extraction using the miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s instruction
Expression of miRNAs by the SYBR Green-based real-time polymerized chain reaction (PCR) method and real-time PCR (StepOnePlus Real-time PCR System, Applied Biosystems, USA)

tag: serum

value: Preeclampsia

value: Female


title: DSP-1001660014867-Y-C12

description: Library name: Sample 180

extract_protocol:
FFPE tissues were parafilm embedded, 5 µM sections were cut with cryostat
Spatial transcritpome sequencing libraries were prepared with Nanostring GeoMx DSP NGS library preparation kit according to manufacturer's instruction


title: Mild preeclampsia 003 T143

description: microRNA Expression


title: Mild preeclampsia 002 T70

description: microRNA Expression


title: Mild preeclampsia 001 T42

description: microRNA Expression


title: DSP-1001660014867-Y-C10

description: Library name: Sample 178


title: DSP-1001660014867-Y-C11

description: Library name: Sample 179


title: DSP-1001660014867-Y-C09

description: Library name: Sample 177


title: DSP-1001660014867-Y-C08

description: Library name: Sample 176


title: Severe preeclampsia 004 T187

description: microRNA Expression

source_name: Severe preeclampsia


title: Severe preeclampsia 003 T142

description: microRNA Expression


title: Severe preeclampsia 002 T76

description: microRNA Expression


title: DSP-1001660014867-Y-C07

description: Library name: Sample 175


title: Severe preeclampsia 001 T53

description: microRNA Expression


title: Healthy 003 T200

description: microRNA Expression

source_name: Healthy

value: Healthy


title: DSP-1001660014867-Y-C04

description: Library name: Sample 172


title: Healthy 002 T167

description: microRNA Expression


title: Healthy 004 T207

description: microRNA Expression


title: DSP-1001660014867-Y-C05

description: Library name: Sample 173


title: DSP-1001660014867-Y-C02

description: Library name: Sample 170


title: DSP-1001660014867-Y-C06

description: Library name: Sample 174


title: DSP-1001660014867-Y-C03

description: Library name: Sample 171


title: Healthy 001 T80

description: microRNA Expression


title: DSP-1001660014867-Y-C01

description: Library name: Sample 169


title: DSP-1001660014867-Y-B12

description: Library name: Sample 168


title: H644B,3P7,replicate 2

city: Guangzhou

first: Huanpeng

last: Chen

state: Guangdong

address: Guangzhou International Bio-Island, Guangzhou, Guangdong, China

institute: Guangzhou National Laboratory

description:
Library name: Sample 5
Column name in All-gene.tpm.anno.xlsx: tpm_H644B

data_processing:
Data filtering: Raw data obtained from sequencing were filtered using the SOAPnuke software (v1.4.0)  to remove: (1) reads containing adapters (adapter contamination); (2) reads with unknown bases (N) exceeding 5% of the read length; (3) low‑quality reads (reads with more than 20% of bases having a quality value below 15). After filtration, clean data were obtained.
Alignment to reference genome: The resulting clean data were aligned to the reference genome sequence using the HISAT software (v2.1.0) .
Alignment to reference gene sequences: The clean data were aligned to the reference gene sequences using the Bowtie2 software (v2.2.5) , and then the RSEM software package (v1.2.8)  was used to calculate gene expression levels for each sample.
Assembly: GRCm38
Supplementary files format and content: All-gene.tpm.anno xlsx file includes tpm for each Sample.

source_name: Primary cells

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2. A total of 1 µg RNA per sample was used for sequencing library construction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 150 bases reads are generated on BGISEQ-500 platform.

treatment_protocol: 3P7-CAR‑T and Ctrl-CAR‑T cells were co-cultured with MC38-Trop2 tumor cells for 48 hours without cytokine supplementation, after which CAR-T cells were sorted by flow cytometry. CAR-T cells were positively selected and subjected to transcription sequencing.

tag: cell type

value: CD3 T cells

value: WT

value: 8 weeks old

tag: strain


title: DSP-1001660014867-Y-B11

city: Dallas

first: Chengsong

institute: UT Southwestern Medical Center

description: Library name: Sample 167


title: H644A,3P7,replicate 1

description:
Library name: Sample 4
Column name in All-gene.tpm.anno.xlsx: tpm_H644A

tag: genotype


title: H500C,Control,replicate 3

description:
Library name: Sample 3
Column name in All-gene.tpm.anno.xlsx: tpm_H500C

value: Ctrl-CAR-T


title: DSP-1001660014867-Y-B09

description: Library name: Sample 165


title: H500B,Control,replicate 2

description:
Library name: Sample 2
Column name in All-gene.tpm.anno.xlsx: tpm_H500B


title: H500A,Control,replicate 1

description:
Library name: Sample 1
Column name in All-gene.tpm.anno.xlsx: tpm_H500A


title: DSP-1001660014867-Y-B07

description: Library name: Sample 163


title: BMPDC_KO3_1.fq.gz

city: Beijing

first: Ruiqun

address: Tsinghua University,Hai Dian, Beijing

institute: Tsinghua University

description: Library name: Sample_6

data_processing:
RNA sequencing was performed using the Illumina HiSeq2500 platform at the Beijing Genomics Institute (BGI, China). Differentially expressed genes were selected based on a P value < 0.05 and a fold change > 1.5.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: fpkm_count_matrix2.xlsx

source_name: Bone marrow

extract_protocol:
For RNA-seq analysis, 2×106 pDCs or BM pDCs were sorted from BM of WT and cKO mice. BM pDCs were centrifuged at 1750 rpm for 5 min at 4°C to remove the supernatant. After resuspending in 1 mL of pre-cooled PBS, the cells were centrifuged again and the supernatant was discarded. To lyse the pDCs, 1 mL of TRNzol RNA extraction reagent was added, and the cells were thoroughly disrupted.
RNA for libraries for RNA-seq were prepared using  polyA_selected

value: Bone marrow

tag: cell line

value: pDCs

value: Plasmacytoid dendritic cells

value: Slc44a3 cKO

value: No


title: DSP-1001660014867-Y-B08

address: 5323 Harry Hines Blvd

description: Library name: Sample 164

value: (v1.0) Human Procode NGS Core Protein, (v1.0) Human NGS Whole Transcriptome Atlas RNA, (v1.1) Human Procode NGS IPA Protein

value: PF


title: DSP-1001660014867-Y-B06

description: Library name: Sample 162


title: BMPDC_KO2_1.fq.gz

description: Library name: Sample_5

value: Slc44a2 cKO


title: BMPDC_KO1_1.fq.gz

description: Library name: Sample_4


title: DSP-1001660014867-Y-B04

description: Library name: Sample 160

value: Desmin


title: DSP-1001660014867-Y-B03

description: Library name: Sample 159


title: BMPDC_WT2_1.fq.gz

description: Library name: Sample_2


title: BMPDC_WT1_1.fq.gz

description: Library name: Sample_1


title: DSP-1001660014867-Y-B01

description: Library name: Sample 157


title: DSP-1001660014867-Y-B02

description: Library name: Sample 158