title: HEK293_WT_RNAseq_rep3

description: pFRT⁄lacZeo and pcDNA™6⁄TR (from the T-REx™ System) stably integrated

data_processing:
Only R1 were used for downstream analysis
fastq files were processed and aligned using the nf-core rnaseq pipeline version 3.6
reads were aligned using STAR and gene level quantification was performed with RSEM
bigwig files for fwd and reverse strand were normalized to DESeq2 size factors
Assembly: Homo sapiens GRCh38 release 95
Supplementary files format and content: bigwig files – normalised to DESeq2 size factors
Supplementary files format and content: tab separated gene counts per sample, RSEM output

extract_protocol:
Total RNA was extracted by TRIzol/chloroform extraction followed by isopropanol precipitation  followed by RiboZero depletion.
Libraries were prepared using KAPA RNA RiboErase HyperPrep kit (KK8581)

treatment_protocol: No treatment

value: Flp-In T-REx HEK295

value: No treatment


title: HT_2

status: Public on Nov 05 2024

type: SRA

city: nanjing

first: rongjian

last: luo

state: jiangsu

address: weigang road No.1

country: China

institute: Nanjing Agricutural University

description:
processed data file: expression_measurements.txt
processed data file: LncRNA_differential_expression.xlsx

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (v1.10) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (v0.10.1).
Valid reads were aligned to the Oryza sativa genome assembly using Hisat (V2.0.4). Then StringTie (v1.3.0) and Ballgown were used to assemble and estimate the expression levels of all transcripts.
CPC (v0.9) and CNCI (v2.0) were used to predict coding potential and LncRNA identification.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: expression_measurements.txt: Tab-delimited text file includes expression measurements (FPKM values) of all transcripts for each Sample.
Supplementary_files_format_and_content: LncRNA_differential_expression.xlsx: Excel file

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Endosperm

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol. The RNAs obtained were quantified and their integrity checked using a Bioanalyzer 2100 device and an RNA 6000 Nano LabChip kit (Agilent, Santa Clara, CA, USA) with RIN number >7.0. A ~10 ug of total RNA was used to deplete the ribosomal RNA fraction, using an Epicentre Ribo-Zero Gold kit (Illumina, San Diego, CA, USA). Following purification, the poly (A)- and poly(A)+ RNA fractions were fragmented by the addition of divalent cations under elevated temperature.
The RNA fragments were reverse-transcribed to create a cDNA library, following the protocol supplied with an Illumina mRNA-Seq sample preparation kit; the average insert size was 300±50bp. Paired-end sequencing was performed by LC-Bio (Hangzhou, China) using an Illumina Hiseq 4000 device.

treatment_protocol: The Japonica rice cultivar NingJing1 (cv. NJ1) raised to the booting stage in the field were removed to a growth chamber delivering a day/night temperature regime of either 36℃/33℃ (HT treatment) or 28℃/25℃ (NT treatment).

tag: cultivar

tag: development stage

value: 10 days after pollination

tag: tissue

value: Endosperm

tag: treatment

value: high temperature


title: SAMP8, 2.5 months old, hippocampus 1

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

country: Italy

institute: Politecnico di Milano

data_processing:
Quality control of the raw data output were examined on FastQC software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt software. UMI were detected and extracted with UMI tools
Trimmed sequence reads were mapped to GRCh38.p13 using STAR
Read count extraction was performed using FeatureCounts
Assembly: GRCm38
Supplementary files format and content: txt file for raw counts extracted with FeatureCounts

organism: Mus musculus

source_name: hippocampus

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer's instructions. RNA quantity and integrity were estimated using the Qubit instrument (Invitrogen, Carlsbad, CA) and the Agilent 4200 TapeStation System (Agilent, Santa Clara, CA).

value: hippocampus

tag: strain


title: SAMP8, 6 months old, hippocampus 1


title: CD19 Cre/+, IgG1, D3, R3

city: Berlin

first: Michela

last: Di Virgilio

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Quality Control
Trimming
Sequence Alignment
Feature counting
bigwig file were generated by BamCoverage
Assembly: mm10
Supplementary files format and content: Tab delimited text file
Supplementary files format and content: bigwig

source_name: Splenocyte

growth_protocol: RPMI medium sup. 10%FBS, SodiumP, AA, 2-ME, L-Glu

extract_protocol:
Trizol
Based on illumina library preparation guideline
Read count extraction

treatment_protocol: LPS, IL4 (IgG1) LPS,TGFB, BAFF (IgG2b)

tag: cell type

value: Splenocyte

tag: genotype

value: CD19 Cre/+


title: HEK293_ARMC5_KO_RNAseq_rep2

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: ARMC5 KO;pFRT⁄lacZeo and pcDNA™6⁄TR (from the T-REx™ System) stably integrated

organism: Homo sapiens

source_name: Human embryonic kidney

growth_protocol: RPMI1DMEM, high glucose,supplemented with 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin

value: Human embryonic kidney

tag: cell line

value: Flp-In T-REx HEK297

value: ARMC5 KO;pFRT/lacZeo and pcDNATM6/TR (from the T-RExTM System) stably integrated


title: HT_3


title: HEK293_ARMC5_KO_TTseq_rep1

description:
ARMC5 KO;pFRT⁄lacZeo and pcDNA™6⁄TR (from the T-REx™ System) stably integrated
Biotinylated nascent RNA

data_processing:
fastq files were processed and aligned using the nf-core rnaseq pipeline version 3.6
reads were aligned using STAR and gene level quantification was performed with RSEM
bigwig files for fwd and reverse strand  were normalized to yeast spike ins
Assembly: Homo sapiens GRCh38 release 95
Supplementary files format and content: bigwig files normalised to yeast spike ins
Library strategy: TTchem-Seq

extract_protocol:
Briefly, 2 millions of WT or ARMC5 KO cells were seeded in 10cm dish, 4SU labeling was performed next day by adding 4SU directly to the tissue culture medium to a final concentration of 1 mM. Incubate the cells with 4SU for 15 min, then medium was removed, and labeling was terminated by addition of 1 mL of TRIzol (Invitrogen, 10296028) per dish. Collect the TRIzol-cell mixture into a microcentrifuge tube. Total RNA was extracted by TRIzol/chloroform extraction followed by isopropanol precipitation.
100 μg of 4SU-labeled mammalian RNA per sample and 1 μg of S. cerevisiae 4TU-labeled RNA were mixed into 100μl total volume of RNase-free water, followed by the addition of 20 μl of 1 M NaOH per sample and incubation for 20 min on ice to fragment the RNA. RNA fragmentation was terminated by addition of 80 μl of 1 M Tris, pH 6.8 per sample and proceed immediately with two rounds clean-up reaction on Micro Bio-Spin P-30 gel columns (Biorad, 7326250) to fully remove NaOH to prevent any further RNA fragmentation. Column purified RNA was biotinylated in a total volume of 250 ml, containing 10 mM Tris-HCl pH 7.4, 1mMEDTA and 5 mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark, then was purified using phenol:chloroform extraction. Then the dissolved RNA was incubated at 65°C to denature, followed by μMACS Streptavidin Kit (Milentyl, 130-074-101) purification according to the manufacturer’s instructions to get pure biotinylated RNA. Biotinylated RNA was cleaned up using the RNeasy MinElute kit (QIAGEN, 74204), after that, the harvested RNA represents nascent RNA which could be used for making sequencing libraries

treatment_protocol: 1 mM 4SU labeling in the medium for 15 min

value: Flp-In T-REx HEK296


title: HT_1


title: HEK293_WT_RNAseq_rep2

value: Flp-In T-REx HEK294

value: pFRT/lacZeo and pcDNATM6/TR (from the T-RExTM System) stably integrated


title: trearment rep4

city: guangzhou

first: wang

last: piao

state: guangdong

address: jingxi street

department: nanfang hospital

institute: southern medical university

description:
treatment (phytic acid)
PA4

data_processing:
DNBSEQ-T7
Cutadapt was used to remove the 3' end of the junction, with the removed portion having at least 10 bp Overlap (AGATCGGAAG) from the known junction, allowing for 20% base mismatches; Reads with an average mass fraction below Q20 were removed
Filtered Reads were compared to the reference genome using the upgraded HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software from TopHat2.
The gene structure annotation information (GTF file) was first read, and then the comparison results were compared with the gene structure and the results were counted.
We used DESeq to differentially analyze gene expression and calculated the differentially expressed ploidy and significance P-value for each gene.
Assembly: mm10
Supplementary files format and content: Text fles include RPKM values for each Sample

source_name: skin

extract_protocol:
RNA was harvested sted using TRIzol reagent (Yeasen).1.3ug 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: skin

value: MC903 plus phytic acid


title: CD19 Cre/+, IgG1, D3, R2


title: HEK293_ARMC5_KO_RNAseq_rep1


title: trearment rep3

description:
treatment (phytic acid)
PA3


title: SAMP8, 2.5 months old, cortex 3

source_name: cortex

value: cortex


title: CD19 Cre/+, IgG1, D3, R1


title: HEK293_WT_RNAseq_rep1

value: Flp-In T-REx HEK293


title: HEK293_ARMC5_KO_RNAseq_rep3

value: Flp-In T-REx HEK298

value: No treatment


title: trearment rep2

description:
treatment (phytic acid)
PA2


title: SAMP8, 2.5 months old, cortex 2


title: CD19 Cre/+, IgG1, D2, R2


title: SAMP8, 6 months old, cortex 3


title: HEK293_ARMC5_KO_PRO_rep2

description:
ARMC5 KO;pFRT/lacZeo and pcDNA™6/TR (from the T-REx™ System) stably integrated
HEK293_ARMC5_KO_PRO_rep2

data_processing:
PRO-seq data were processed using a pipeline adapted from Cosby et al, 2021 [1] available from Zenodo https://zenodo.org/record/4019173#.Y4XvF3bP1aQ
UMIs were extracted and trimmed using fastp v0.23.3
Ribosomal reads were dropped from further analysis by alignment against Ensembl human rDNA repeats using bowtie2 v2.4.4 (--fast-local), retaining just the unmapped reads.  Remaining reads were mapped to the spike-in Drosophila melanogaster Dm6 assembly using bowtie2 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant) and to the target Homo sapiens GRCh38 genome assembly also using bowtie2 (--local --sensitive-local)
PCR duplicates were removed from each BAM file using UMI-tools, applying the “directional” method
Strand-specific bigWig coverage tracks limited to the single base of each read mate-pair representing the 3’end of the nascent RNA were created per target genome sample using deepTools’ bamCoverage function [6] (forward: --samFlagInclude 82, --Offset 1 –binSize 1, reverse: --samFlagInclude 82, --Offset 1 –binSize 1)
Assembly: GRCh38
Supplementary files format and content: bigwig - normalised coverage of 3' end of nascent RNA
Library strategy: PRO-seq (Precision Run-On sequencing)

source_name: Flp-In T-REx HEK293

growth_protocol: DMEM, high glucose,supplemented with 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin

extract_protocol:
Briefly, both WT or ARMC5 KO human cells and Drosophila S2 cells were permeabilized to get the nuclei and count numbers. 1 millon nuclei from WT or ARMC5 KO cells per sample were mixed with 2% spike-in Drosophila S2 nuclei in 50 μL volume, then mixed with 50 μL 2X Run-On Master Mix containing 4 biotin-tagged NTPs (PerkinElmer, NEL542001EA-NEL545001EA). Run-on reaction was incubated at 37°C for 5 min, then was terminated by immediately adding TRIzol LS followed by total RNA extraction.
Total RNA was denatured by NaOH and purified by Bio-Rad RNase free P-30 column following manufacturer’s instructions, then 3’ RNA adaptor ligation was performed. After 3’ RNA adaptor ligation, biotin labeled RNA was enriched by Streptavidin beads. 5’ Hydroxyl repair and decapping reaction were performed on-bead followed by 5’ RNA adaptor ligation. After these enzymatic reactions, Streptavidin beads with biotin labeled RNA was washed. Biotin labeled RNA was extracted from Streptavidin beads using TRIzol/chloroform extraction then reverse transcription was performed off-bead to get cDNA.  1.54 µL out of the 20 µL reverse transcription reaction was used to do the test amplification (qPCR) to determine the amplification cycle number, then full-scale amplification was performed with desired number of cycles. PCR products were cleaned up and selected by SPRI beads for sequencing.


title: HEK293_ARMC5_KO_PRO_rep3

description:
ARMC5 KO;pFRT/lacZeo and pcDNA™6/TR (from the T-REx™ System) stably integrated
HEK293_ARMC5_KO_PRO_rep3


title: CD19 Cre/+, IgG1, D4, R1


title: trearment rep1

description:
treatment (phytic acid)
PA1


title: RIF1 F/F CD19 Cre/+, IgG1, D4, R3

value: RIF1 F/F CD19 Cre/+


title: HEK293_ARMC5_KO_PRO_rep1

description:
ARMC5 KO;pFRT/lacZeo and pcDNA™6/TR (from the T-REx™ System) stably integrated
HEK293_ARMC5_KO_PRO_rep1


title: SAMP8, 6 months old, cortex 2


title: control rep4

description:
control
AD4


title: control rep3

description:
control
AD3


title: SAMP8, 9 months old, cortex 4


title: HEK293_WT_PRO_rep3

description:
pFRT/lacZeo and pcDNA™6/TR (from the T-REx™ System) stably integrated
HEK293_WT_PRO_rep3


title: SAMP8, 9 months old, hippocampus 1


title: CD19 Cre/+, IgG1, D2, R1


title: HEK293_WT_PRO_rep2

description:
pFRT/lacZeo and pcDNA™6/TR (from the T-REx™ System) stably integrated
HEK293_WT_PRO_rep2


title: CD19 Cre/+, IgG1, D2, R3


title: control rep1

description:
control
AD1


title: SAMP8, 6 months old, cortex 4


title: RIF1 F/F CD19 Cre/+, IgG1, D4, R2


title: RIF1 F/F CD19 Cre/+, IgG1, D4, R1


title: control rep2

description:
control
AD2


title: SAMP8, 9 months old, cortex 3


title: SAMP8, 9 months old, cortex 2


title: RIF1 F/F CD19 Cre/+, IgG1, D3, R3


title: P3032 NS_32

city: Seoul

first: Hae-Ock

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Department of Microbiology

country: South Korea

institute: College of Medicine, The Catholic University of Korea

description:
NS_32
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were mapped to the GRCh38 human reference genome using the Cell Ranger toolkit (version 5.0.0).
Assembly: GRCh38
Supplementary files format and content: R object file

source_name: Normal Brain

extract_protocol:
Single-cell isolation was performed differently depending on the samples. (1) Biopsy samples and normal lymph node tissues were chopped into 2-4mm pieces and dissociated in an enzyme solution containing collagenase/hyaluronidase (STEMCELL Technologies, Vancouver, Canada) and DNase I, RNase-Free (lyophilized) (QIAGEN, Hilden, Germany) at 37 °C for 1 h. Tissue pieces were re-mixed by gentle pipetting at 20 min intervals during the incubation. (2) Tumor and normal lung tissue dissociation was performed using a tumor dissociation kit (Miltenyi Biotech, Germany) following the manufacturer’s instructions. Briefly, tissue was cut into 2–4 mm pieces and transferred to a C tube containing the enzyme mix (enzymes H, R, and A in RPMI1640 medium). The GentleMACS programs h_tumor_01, h_tumor_02, and h_tumor_02 were run with two 30-min incubations on the MACSmix tube rotator at 37 °C. (3) Brain tissue was chopped into 2–4 mm pieces and incubated in an enzyme solution (collagenase (Gibco, Waltham, MA, USA), DNase I (Roche, Basel, Switzerland), and Dispase I (Gibco, Waltham, MA, USA) in DMEM) at 37 °C for 1 hour. Tissue pieces were re-mixed by gentle pipetting at 15 min intervals during the incubation. (4) Pleural fluids were transferred to a 50-ml tube, and cells spun down at 300 g.  Each cell suspension was transferred to a new 50 ml (15 ml for biopsy samples) tube through a 70-µm strainer. The volume in the tube was readjusted to 50 ml (or 15 ml) with RPMI1640 medium, and spun down to remove the enzymes. The supernatant was aspirated out, the cell pellet was resuspended in 4 ml of RPMI1640 medium, and dead cells were removed using Ficoll-Paque PLUS (GE Healthcare, Chicago, IL, USA) separation.   For the samples subjected to a multiplexing, dissociated cells were cryopreserved in CELLBANKER1 (Zenogen, Fukushima, Japan) and thawed for pooling.
Single-cell suspensions were loaded into the Chromium system (10x Genomics, Pleasanton, CA, USA). Following the manufacturer’s instructions, 3’ scRNA-seq libraries for fourteen samples were generated using Chromium Single Cell 3′ v2 Reagent Kits. The 3’ library preparation for a sample (EBUS_119) used Chromium Single Cell 3′ v3 Reagent Kits. The 5’ scRNA-seq libraries for twelve individual and two pooled samples were generated using Chromium Single Cell 5′ v2 Reagent Kit. Libraries were then sequenced on an Illumina HiSeq 2500 for 3’ scRNA-seq and an Illumina NovaSeq 6000 for 5’ scRNA-seq.

tag: patient

value: Normal Brain

tag: tumor stage

value: IV

tag: cancer subtype

value: ADC

tag: recist

value: PR

tag: platform

value: Single Cell 5'


title: HEK293_WT_PRO_rep1

description:
pFRT/lacZeo and pcDNA™6/TR (from the T-REx™ System) stably integrated
HEK293_WT_PRO_rep1

value: Human embryonic kidney


title: SAMP8, 9 months old, cortex 1


title: RIF1 F/F CD19 Cre/+, IgG1, D3, R2

value: Splenocyte


title: P2009 LN_09

description:
LN_09
10x Genomics

source_name: Normal LN

value: Normal LN

value: IB


title: 6.6._dPacR_t=12

city: Turku

first: Yagut

last: Allahverdiyeva

address: Tykistönkatu 6A

department: Life Sciences

country: Finland

institute: Turku University

data_processing:
The sequencing platform used was DNBseq with a read length of PE 100bp. After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads (via the SOAPnuke software from BGI as a service).
The provided data was analyzed via the Chipster software
Initial Trimming of reads with FastX was performed
Alignment with TopHat2 for paired end reads and own genome (library type: first-strand, expected inner distance between mate pairs: 24, ignore novel junctions: yes, Sanger Phred+33, standard deviation for the inner distances between mate pairs: 85, how many hits is a read allowed to have: 20, number of mismatches allowed in final alignment: 2, minimum anchor length: 8, maximum number od mismatches allowed in anchor: 0, minim intron length: 70, maximum intron length: 500000, report only paired alignments: yes)
aligned reads per genes were counted with HTSeq using own GTF file (mode to handle reads overlapping more than one gene: union, minimum alignment quality: 10, feature type to count: exon, feature ID to use: gene_id)
Differential expression was analyzed using DESeq2 (cutoff p-value: 0.05, method for estimating size factors: ratio)
For experiential quality control, PCA analysis was performed. Principal component 1 (PC1) accounts for 83-86% of variance between the CS and ΔpacR replicates. When comparing CS or ΔpacR data between timepoints, 90-93% of variance was accounted for by PC1.
gene-body coverage at the 5’ end was higher than at the 3’ end, which could point towards a sequencing-bias in favor of the 5’ end of the RNA
Assembly: nostoc_sp_pcc_7120_fachb_418_gca_000009705, version ASM970v1_, current ENSEMBL release (October 2023)
Supplementary files format and content: tab-delimited text file with raw counts for each sample

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: all cells

growth_protocol: The ΔpacR deletion mutant of the Anabaena sp. PCC7120 wild type strain (CSS74) and control strain with a spectinomycin resistance cassette (CSS77) were described previously (Picossi et al., 2015). The starting cultures were maintained in  BG11 medium buffered with 20 mm HEPES-NaOH (pH 7.5) and supplemented  with 25 ug/ml of spectinomycin. The cultures were grown at 30°C with 1% CO2, ~50 µmol photons m-2 s-1, and agitated at 80 rpm. Pre-cultures were generated by harvesting cells from starting cultures after 4 days and resuspending cells at OD750=0.1. Cells were then grown for 4 days in BG110 medium buffered with 20 mm HEPES-NaOH (pH 7.5) supplemented with 6mM NH4Cl on day 0, and additional 3mM NH4Cl was supplemented on days 2 and 3.

extract_protocol:
Total RNA was isolated using  the hot-phenol method. DNAse treatment was performed with the Invitrogen kit. RNA concentration was measured with DS-11+ spectrophotometer (DeNovix) and 3ug of RNA from each sample was sent to BGI (China) for RNA-sequencing.
Library construction was performed as a service by BGI

treatment_protocol: Experimental cultures were generated similar to precultures, however cells were harvested by filtration and washed twice with the new medium, and then grown in BG110 medium (pH 7.5) supplemented with either 3mM NH4+ or 17.6 mM NO3- as the nitrogen source.

value: all cells

value: all cell types

value: Anabaena sp. PCC7120 strain CSS74 containing all3953 knock-out

value: NO3- containing medium, 12h


title: 6.6._dPacR_t=1

value: NO3- containing medium, 1h


title: P2016 LN_16

description:
LN_16
10x Genomics

value: IIB

value: SQ

value: PD


title: 6.6._dPacR_t=0

value: NH4+ containing medium


title: SAMP8, 2.5 months old, cortex 1

value: cortex


title: 6.6._CS_t=12

value: Anabaena sp. PCC7120 strain CSS77 containing C.S3 gene cassette


title: SAMP8, 6 months old, cortex 1


title: P1072 EBUS_72

description:
EBUS_72
10x Genomics

source_name: LN

value: LN

value: ED

value: SCLC

value: NE


title: RIF1 F/F CD19 Cre/+, IgG1, D2, R2

value: Splenocyte

value: RIF1 F/F CD19 Cre/+


title: 6.6._CS_t=1

value: all cells


title: P1079 EBUS_79

description:
EBUS_79
10x Genomics

value: IV

value: ADC

value: Single Cell 5'


title: 6.6._CS_t=0

value: all cell types


title: RIF1 F/F CD19 Cre/+, IgG1, D2, R1


title: Liver_ZT10_DKO_REV-ERBalpha-WT_RNA-seq_rep4

city: Philadelphia

first: KUN

last: ZHU

state: PA

address: 3400 Civic Center Blvd, SCTR-12-196

country: USA

institute: University of Pennsylvania

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output
RNA-seq fastq data was mapped by STAR aligner 2.7.1a
Low MAPQ (<=30) were removed by samtools 1.9
featureCounts v2.0.1 and DEseq2 1.36.0 were used to determine differential expressed genes
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted by Trizol reagent from frozen liver tissue and purified by RNeasy Mini Kit.
For RNA-seq, 1 ug total RNA extracted from each biological replicated liver was used for library construction according to TruSeq Stranded Total RNA Library Prep kit protocol

value: Liver

value: REV-ERBalpha re-expressing


title: 27.5._dPacR_t=12

value: Anabaena sp. PCC7120 strain CSS74 containing all3953 knock-out

value: NO3- containing medium, 12h


title: Liver_ZT10_DKO_REV-ERBalpha-WT_RNA-seq_rep3


title: P1018 EBUS_18

description:
EBUS_18
10x Genomics

source_name: Bronchus

value: Bronchus


title: P1063 BRONCHO_63

description:
BRONCHO_63
10x Genomics


title: Postnatal Day 14 Rep 2

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
TPM values generated from counts obtaind from HTseq and DESeq2
Gene Ontology was determined using DAVID_6.8
Assembly: GRCm38 vM24 mm10 (mus musculus)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

extract_protocol:
Hepatocytes were isolated from normal fed 10-12 week old mice. Additionally, hepatocytes were isolated from P14 livers. From all samples total RNA was isolated and after polyA selection sequenced on an Illumina platform.
Truseq stranded Illumina kit was used to make libraries

value: Hepatocytes

value: WT

tag: age


title: Liver_ZT10_DKO_REV-ERBalpha-WT_RNA-seq_rep2


title: P1084 EBUS_84

description:
EBUS_84
10x Genomics

value: LN


title: RIF1 F/F CD19 Cre/+, IgG1, D3, R1


title: Postnatal Day 14 Rep 1


title: mLEC-nciLT+anti-LTbR Ab/CL4h-1-2-3

type: RNA

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description: Gene expression data fromnciLT pretreated and 4h 3C8/CL treated primary mouse lymphatic endothelial cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hours at 45oC on GeneChip mouse and human Affymetrix gene ST2 arrays.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip system 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: primary mouse lymphatic endothelial cells pretreated with 20 mM nciLT then with 2 mg/mL anti-LTbR Ab/CL for 4 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 3x105 mLECs in mEC medium containing VGEF, EGF plated in 12-well TC for overnight before stimulation

extract_protocol: Qiagen Rneasy mini plus kit used for total RNA extraction and performed according to the manufacturer's instructions. Residual DNA was removed with on-column DNase treatment (Qiagen). Highly purified RNA (A260/A280 ratio between 1.9–2.1) with RIN (RNA integrity number) >7.0

treatment_protocol: mLECs pretreated with 20 uM each peptide at 37oC for 30 min. washed and incubated with 2 ug/mL rat anti-LTbR agonist Ab (3C8) at 4oC for 30 min, then crosslink (CL) with 2 ug/mL anti-rat IgG at 37oC for 4 hours.


title: RIF1 F/F CD19 Cre/+, IgG1, D2, R3


title: mLEC-anti-LTbR Ab/CL 4h 1-2-3

description: Gene expression data from4h 3C8/CL treated primary mouse lymphatic endothelial cells

source_name: primary mouse lymphatic endothelial cells treated with 2 mg/mL anti-LTbR Ab/CL for 4 hours


title: Liver_ZT10_DKO_REV-ERBalpha-WT_RNA-seq_rep1


title: P1016 LM_16

description:
LM_16
10x Genomics

value: ED

value: SCLC

value: PR


title: ESRP2 KO Rep2

value: ESRP2 KO


title: 27.5._CS_t=12

value: all cells

value: Anabaena sp. PCC7120 strain CSS77 containing C.S3 gene cassette


title: Liver_ZT10_DKO_YFP_RNA-seq_rep4

value: REV-ERBs double-knockout


title: P1016 EBUS_16

description:
EBUS_16
10x Genomics

value: Single Cell 5'


title: mLEC-medium-1-2-3

description: Gene expression data from untreated primary mouse lymphatic endothelial cells

source_name: primary mouse lymphatic endothelial cells without treatment


title: mLEC-ciLT+anti-LTbR Ab/CL4h-1-2-3

description: Gene expression data from ciLT pretreated and 4h 3C8/CL treated primary mouse lymphatic endothelial cells

source_name: primary mouse lymphatic endothelial cells pretreated with 20 mM ciLT then with 2 mg/mL anti-LTbR Ab/CL for 4 hours


title: ESRP2 KO Rep1


title: P1063 EBUS_63

description:
EBUS_63
10x Genomics

value: IV

value: ADC

value: NE


title: Liver_ZT10_DKO_YFP_RNA-seq_rep3

value: Liver


title: 27.5._CS_t=0

value: all cell types

value: NH4+ containing medium


title: P1062 EBUS_62

description:
EBUS_62
10x Genomics

value: PD


title: 27.5._dPacR_t=1

value: Anabaena sp. PCC7120 strain CSS74 containing all3953 knock-out

value: NO3- containing medium, 1h


title: ESRP2 WT Rep 3

value: Hepatocytes

value: WT


title: P1030 EBUS_30

description:
EBUS_30
10x Genomics

value: LN


title: Liver_ZT10_DKO_YFP_RNA-seq_rep2


title: P4001 PCNB_01

description:
PCNB_01
10x Genomics

source_name: Lung

value: Lung

value: SD


title: ESRP2 WT Rep 2


title: 26.5._dPacR_t=1

value: all cells


title: 27.5._dPacR_t=0


title: 26.5._dPacR_t=12

value: NO3- containing medium, 12h


title: P1017 LM_17

description:
LM_17
10x Genomics

value: SQ

value: Single Cell 5'


title: Liver_ZT10_DKO_YFP_RNA-seq_rep1

value: REV-ERBs double-knockout


title: ESRP2 WT Rep 1


title: Liver_ZT10_YFP_RNA-seq_rep3

value: wildtype


title: 27.5._CS_t=1

value: Anabaena sp. PCC7120 strain CSS77 containing C.S3 gene cassette


title: MIXED

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

institute: IRCCS, Ospedale San Raffaele

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
The whitelist of cell barcodes was identified with 'umi_tools whitelist --set-cell-number 4000 --bc-pattern=CCCCCCCCCCCCNNNNNNNN' (umi_tools v1.0.0).
Reads of the whitelisted cells were extracted with 'umi_tools extract --bc-pattern=CCCCCCCCCCCCNNNNNNNN --filter-cell-barcode --whitelist=whitelist.txt' (umi_tools v1.0.0).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of human genome (GRCh38) with parameter '--outFilterMultimapNmax 1' (to exclude multi-mapping reads).
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation for GRCh38 (version 27) using Subread featureCounts (v1.6.4). Results were saved in BAM files with option 'featureCounts -R BAM' and succesively sorted and indexed with samtools (v1.9).
Per gene counts were summarized for each cell using 'umi_tools count --per-gene --gene-tag=XT --per-cell --wide-format-cell-counts' (umi_tools v1.0.0).
Genome_build: hg38 (GRCh38 - v27)
Supplementary_files_format_and_content: Tab separated files of raw counts; matrix with UMI_BARCODES on the columns and genes on the rows.  One file per sample, gzipped (.gz).

source_name: coculture of multiple myeloma B lymphoblasts and bone marrow stromal cells

growth_protocol: Approximately 2.e6 MM.1S and HS-5 cells from independent cultures and 2.e6 cells from 4 hour MM.1S-HS-5 co-culture were washed with PBS+0,01% BSA, filtered with 40μm strainer and resuspended to 200 cell/μl. Approximately 4,000 cells per experimental point have been sequenced at an average of 4.5e4 reads/cell.

extract_protocol: DropSeq (Macosko et al. 2015)

value: cells in coculture

value: coculture of MM.1S and HS-5


title: 26.5._dPacR_t=0

value: all cell types

value: NH4+ containing medium


title: P1090 EBUS_90

description:
EBUS_90
10x Genomics

value: IIIA

value: PR


title: P1017 EBUS_17

description:
EBUS_17
10x Genomics

value: IV


title: 26.5._CS_t=1

value: NO3- containing medium, 1h


title: MM1_S

source_name: multiple myeloma B lymphoblasts

value: multiple myeloma


title: Liver_ZT10_YFP_RNA-seq_rep4

value: Liver


title: Liver_ZT10_YFP_RNA-seq_rep1


title: HS_5

source_name: bone marrow stromal cells

value: stromal cells


title: 26.5._CS_t=0

value: all cells


title: Liver_ZT10_YFP_RNA-seq_rep2


title: P1027 EBUS_27

description:
EBUS_27
10x Genomics

value: LN

value: ADC


title: S. aureus, biofilm and planktonic, BaSSSh-seq 1-4

status: Public on Nov 04 2024

city: Omaha

first: Lee

middle: Erik

last: Korshoj

state: NE

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

description:
BP_BF_count_mat.txt.gz
BP_P_count_mat.txt.gz
gene_names_ids_comp.txt
gene_RS.txt

data_processing:
Cutadapt used for removing adapters; UMI-tools used for extracting UMIs; Cutadapt used for demultiplexing reads; STAR used for alignment to S. aureus USA300 FPR3757 genome (NCBI); featureCounts used for counting reads; UMI-tools used for deduplicating reads based on UMI and mapping coordinates to yield final count matrices
Assembly: S. aureus USA300 FPR3757
Supplementary files format and content: Count matrices (.txt files) are set up as cells (rows) by gene counts (columns) to be read into a Scanpy AnnData object via the read_text function. Gene lists and S. aureus USA300 locus tag numbers are also provided (.txt files) and correspond to the order of genes in the count matrices (columns)

organism: Staphylococcus aureus

source_name: bacterial

growth_protocol: Planktonic: exponential phase, shaking, aerobic, 37°C, RPMI-based medium; Biofilm: 4 days, static, aerobic, 37°C, RPMI-based medium

extract_protocol:
RNA via in-cell split-pool barcoding
Second strand synthesis, rRNA depletion, fragmentation, ligation, and final amplification yielding Illumina sequencing libraries with P5/P7 ends
scRNA-seq (BaSSSh-seq)

treatment_protocol: Planktonic cultures were grown without specific treatment. Biofilms were grown either without treatment (control) or were directly co-cultured with 500,000 macrophages, granulocytic myeloid-derived supressor cells, or neutrophils for 2 h.

value: bacterial

tag: group

value: biofilm and planktonic


title: S. aureus, biofilm-leukocyte co-cultures, BaSSSh-seq 1-4

description:
B_BF_count_mat.txt.gz
B_BFmac_count_mat.txt.gz
B_BFmdsc_count_mat.txt.gz
B_BFpmn_count_mat.txt.gz
gene_names_ids_comp.txt

value: biofilm-leukocyte co-cultures


title: PBMC, low, 378, H3K27ac

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

library_source: genomic

data_processing:
ChIP sequencing data was aligned to human genome hg38 with BWA. Samtools was used to filter reads with a quality score lower than 20, and PCR duplicates were removed with Picard. Peaks were identified with MACS 2.2.6 in paired-end mode and ‘call-summits’ enabled at a false discovery rate of 0.01. A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in each sample. Bigwig files were generated using bam2bw. Count matrix data was loaded to R programming language and differential H3K4me3 loci were identified by using R package edgeR. The confident H3K4me3 signals (Counts per million (CPM) > 1 in more than 2 samples) were used for downstream analysis and Trimmed Mean of M-values (TMM) normalization was performed. Then it was adjusted for differences between donors by an additive linear model with donor as the blocking factor and the dispersion was estimated. The differential H3K4me3 signals were identified by fitting negative binominal generalized linear models. The H3K4me3 signals with p value < 0.01 were subjected to gene ontology analysis. The annotation of H3K4me3 signals were performed with R packages ChIPSeeker and clusterProfiler.
Assembly: hg38
Supplementary files format and content: bigWig, continuous data for display in genome browser

molecule: genomic DNA

source_name: PBMCs

extract_protocol:
PBMCs were resuspended in RPMI culture medium and fixed using formaldehyde (1% final concentration, Sigma Aldrich) for 10 minutes at room temperature. Unreacted formaldehyde was quenched with 125 mM glycine and incubated for 5 minutes at room temperature. Cells were washed twice in PBS containing protease inhibitor cocktail (Roche) and 1 mM PMSF (Roche), and subsequently snap frozen in liquid nitrogen. Cell pellets were stored at -80°C for further use. Cells were sonicated at a concentration of 15 million cells/mL using a Bioruptor pico sonicator (Diagenode; 10-20 cycles, 30s on, 30s off), at 4°C. Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to manufacturer’s instruction. In short, 500,000 cells were incubated overnight with 1 mg H3K4me3 (Diagenode) and protein A magnetic beads at 4°C. Beads and chromatin/antibody mixture were washed four times for 5 minutes at 4°C. After washing chromatin was eluted and proteins were degraded using proteinase K. DNA was purified using spin columns and eluted in millliQ.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. 2.5 mL of the NEXTflex adaptor stock (600 nM, Bio Scientific) was used for adaptor ligation of each sample. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up used to ensure proper removal of adapters. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced to a read length of 50 bp on an Illumina NextSeq500.

value: PBMCs

tag: chip antibody

value: H3K27ac (Diagenode #pAb-196-050)


title: PBMC, high, 250, H3K27ac


title: Loss of Y chromosome, Pool2

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: other

data_processing:
Fastqs were generated using CellRanger v7.2 mkfastq
Reads were aligned to the Flex probeset v1.0.1 reference using CellRanger v7.2
Assembly: N/A (probe set v.1.0.1)
Supplementary files format and content: Probe barcode (csv) shows the sample ID
Supplementary files format and content: h5 files representing probe gene expression counts

molecule: other

source_name: peripheral blood mononuclear cells

extract_protocol:
cDNA was extracted according to the 10x Genomics Flex scRNA-seq workflow. Libraries were constructed according to 10x Genomics Flex workflow; R1 is technical barcode sequence; R2 is the probe barcode sequences
10x Genomics Flex

value: peripheral blood mononuclear cells

value: Germline XY donors


title: Loss of Y chromosome, Pool1


title: 26.5._CS_t=12

value: all cell types

value: Anabaena sp. PCC7120 strain CSS77 containing C.S3 gene cassette

value: NO3- containing medium, 12h


title: PBMC, high, 233, H3K27ac


title: PBMC, low, 242, H3K27ac


title: PBMC, low, 244, H3K27ac


title: PBMC, low, 230, H3K27ac


title: PBMC, high, 226, H3K27ac


title: PBMC, high, 220, H3K27ac


title: PBMC, high, 196, H3K27ac


title: PBMC, high, 197, H3K27ac


title: PBMC, low, 378, H3K4me3

value: H3K4me3 (Diagenode #pab-003-050)


title: PBMC, high, 250, H3K4me3


title: PBMC, low, 243, H3K4me3


title: PBMC, low, 242, H3K4me3


title: PBMC, high, 233, H3K4me3


title: PBMC, low, 229, H3K4me3


title: PBMC, low, 230, H3K4me3


title: PBMC, high, 196, H3K4me3


title: PBMC, high, 197, H3K4me3


title: PBMC, high, 220, H3K4me3


title: PBMC, low, 378

data_processing:
RNA bulk sequencing was performed by Single Cell Discoveries (Utrecht, The Netherlands) with a sequencing depth of 20 million reads/sample. Library preparation was performed according to the CEL-seq2 protocol. Sequencing was performed on a Nextseq500 (Illumina) and mapped using star.
Assembly: HG38
Supplementary files format and content: RNAcounts_Transplantation text file includes raw files for each sample

extract_protocol:
RNA was isolated from 1*10^6 PBMCs using RNeasy Mini kit (Qiagen) including DNAse I digestion according to manufacturer’s instructions.
RNA bulk sequencing was performed by Single Cell Discoveries (Utrecht, The Netherlands) with a sequencing depth of 20 million reads/sample. Library preparation was performed according to the CEL-seq2 protocol. Sequencing was performed on a Nextseq500 (Illumina).


title: PBMC, low, 243


title: PBMC, high, 250


title: PBMC, low, 244


title: PBMC, low, 242


title: PBMC, low, 243, H3K27ac


title: PBMC, low, 229, H3K27ac


title: PBMC, low, 230


title: PBMC, high, 226


title: PBMC, low, 229


title: PBMC, high, 197


title: PBMC, high, 220


title: PBMC, high, 233


title: PBMC, high, 196


title: A673, sh908 doxycycline positive, rep3

city: Nantes

first: Anaïs

last: Postec

address: 1 Rue Gaston Veil

country: France

institute: Nantes University

description: sh908 target is KCNN1. Activated in this sample.

data_processing:
fastp v.0.19.5 (parameters: default + «--detect_adapter_for_pe -q 30»)
kallisto quant v.0.46.2 (parameters: default + «-b 100»)
Assembly: hg38 (GRCh38.p14 analysis set) and Refseq GCF_000001405.40
Supplementary files format and content: «abundance.tsv» files are the output of kallisto quant. It determines the expression of each transcript within the sample.

source_name: cell line

extract_protocol:
NucleoSpin RNA Plus Kit (Macherey-Nagel)
Illumina TruSeq Stranded mRNA Sample Preparation kit

value: cell line

value: ewing sarcoma

value: doxycyxline added


title: A673, sh908 doxycycline negative, rep2

description: sh908 target is KCNN1. Not activated in this sample.

value: doxycyxline not added


title: PBMC, low, 244, H3K4me3


title: PBMC, high, 226, H3K4me3


title: A673, sh908 doxycycline positive, rep1


title: A673, sh908 doxycycline positive, rep2


title: U2OS, rep1

value: U2OS (RRID:CVCL_0042)

value: osteosarcoma


title: U2OS, rep2


title: A673, sh908 doxycycline negative, rep3


title: SAOS2, rep2

value: SaOS-2 (RRID:CVCL_0548)


title: SAOS2, rep3


title: A673, sh908 doxycycline negative, rep1


title: SAOS2, rep1


title: MG63, rep1


title: KHOS, rep2

value: KHOS/NP (RRID:CVCL_2546)


title: MG63, rep2


title: KHOS, rep1


title: KHOS, rep3


title: HOS-MNNG, rep2

value: MNNG/HOS Cl #5 (RRID:CVCL_0439)


title: HOS-MNNG, rep1


title: G292, rep3

value: G-292 clone A141B1 (RRID:CVCL_2909)


title: TC71, rep2


title: G292, rep1


title: G292, rep2


title: TC71, rep3


title: ATO3

city: Tianjin

first: Shijiao

last: Cai

address: 154 Anshan Road,Heping District

department: Department of Pharmacy

institute: Tianjin Medical University General Hospital

data_processing:
lllumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequen then mapped to rn6 whole genome using HISAT2.
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie.
Gene counts were normalized using geometric mean in DESeq2 package.
Differential gene expression by DEseq2 was performed on normalized gene counts.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: colon

growth_protocol: Female  C57BL/6 J mice were used as experimental an_x0002_imals and housed in a specific pathogen-free animal facility under controlled environmental conditions with 12 h light-dark cycle.

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

treatment_protocol: The normal group was treated by gavage with the vehicle alone (0.5% CMC-Na)for consecutive 7 days.The model group was treated by gavage with 5 % DSS solution for consecutive 7 days. The atorvastatin group was treated by gavage with 10 mg/ kg atorvastatin. Atorvastatin was administered strictly once daily for 5 days in a volume of 0.2 mL from day 3 to day 7.

value: colon

value: WT

value: 10 mg/ kg atorvastatin

value: C57BL/6 J

tag: Sex

value: female


title: TC71, rep1


title: ATO2


title: patch-seq sample_S314

city: Houston

first: Junzhan

last: Jing

state: Texas

address: 1250 Moursund St., Suite 0925

department: Neuroscience

institute: Baylor College of Medicine

description: patchseq.mtx.csv

data_processing:
snRNA-seq,  Cell Ranger (version 5.0.1) with the Mus musculus genome (GRCm38) and annotation GTF (version M23) was used to generate the output count matrix.
patchseq, raw reads were aligned to the  Mus musculus genome (GRCm38) with annotation GTF (version M23) using STAR 2.7.7a  and an expression matrix was generated with FeatureCounts
Assembly: Mus musculus genome (GRCm38) with annotation GTF (version M23)
Supplementary files format and content: HDF5 Format raw count files generated by Cell Ranger (version 5.0.1)
Supplementary files format and content: patchseq raw count csv file, coma-delimited text file, column names are cell_ids , row names are gene symbols

source_name: cochlear nucleus

extract_protocol:
Single nucleus extraction and patchseq RNA
10x Genomics Chromium Next GEM Single Cell 3'v3 and Smart-seq2

value: cochlear nucleus


title: ATO1


title: patch-seq sample_S313

description: patchseq.mtx.csv


title: U2OS, rep3


title: SKES1, rep3

value: SK-ES-1 (RRID:CVCL_0627)


title: Model3

value: 5 % DSS


title: MG63, rep3

value: cell line


title: patch-seq sample_S312

description: patchseq.mtx.csv


title: Model2


title: SKES1, rep2

value: ewing sarcoma


title: Model1


title: patch-seq sample_S311

description: patchseq.mtx.csv


title: Normal3

value: 0.5% CMC-Na


title: HOS-MNNG, rep3


title: patch-seq sample_S310

description: patchseq.mtx.csv


title: Normal2


title: SKES1, rep1


title: Normal1


title: patch-seq sample_S308

description: patchseq.mtx.csv


title: Blood, CAD vaccine immunized, Day 1，rep2

city: Shanghai

first: Fan

last: Zhao

address: 160 Baseng Road, Pudong New District

institute: R&R Therapeutic  Co., Ltd.

data_processing:
Quality control: Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
Reads mapping: The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Expression analysis:we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Differential expression analysis:Then difference expression of genes was analyzed by DESeq (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, we used R language Pheatmap (v1.0.12) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Enrichment analysis: we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO (v2.50.0) to perform GO enrichment analysis on the differential genes (all DEGs / up DEGs / down DEGs), calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. Gene Set Enrichment Analysis (GSEA) (v4.1.0) tool was used for GSEA enrichment analysis of all genes, and GSEA enrichment analysis pathway map was drawn.
Assembly: GRCm39
Supplementary files format and content: Excel files include raw counts for each sample
Supplementary files format and content: Excel files include RPKM for each sample

source_name: blood

extract_protocol:
Total RNA was isolated from samples using the Trizol Reagent (Invitrogen Life Technologies). Following extraction, the concentration, quality, and integrity of the RNA were assessed using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were then used as input material for the RNA sample preparations. mRNA was purified from the total RNA using poly-T oligo-attached magnetic beads to selectively isolate polyA RNA for subsequent sequencing.
Sequencing libraries were constructed by purifying mRNA from total RNA using poly-T oligo-attached magnetic beads. The RNA was fragmented with divalent cations in an Illumina proprietary buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II, followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. Overhangs were converted to blunt ends, and the enzymes were removed. After adenylation of the 3' ends, Illumina PE adapter oligonucleotides were ligated. cDNA fragments of 400-500 bp were purified using the AMPure XP system. DNA fragments with ligated adapters were enriched using Illumina PCR Primer Cocktail in a 15-cycle PCR reaction. The products were purified and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system.

treatment_protocol: Blood samples from mice were collected for analysis before and after vaccination

value: blood

value: blood-brone Leukocytes

tag: time

value: Day 1

value: Vaccinated


title: RDES, rep2

value: RD-ES (RRID:CVCL_2169)


title: RDES, rep1


title: patch-seq sample_S307

description: patchseq.mtx.csv


title: Blood, CAD vaccine immunized, pre-immunization (Day 0)，rep3

value: Day 0

value: Untreated


title: Blood, CAD vaccine immunized, pre-immunization (Day 0)，rep2


title: patch-seq sample_S306

description: patchseq.mtx.csv


title: Blood, CAD vaccine immunized, Day 1，rep1


title: Blood, CAD vaccine immunized, pre-immunization (Day 0)，rep1


title: patch-seq sample_S304

description: patchseq.mtx.csv


title: Blood, SP vaccine immunized, Day 1，rep2


title: Blood, SP vaccine immunized, Day 1，rep3


title: MHHES1, rep2

value: MHH-ES-1 (RRID:CVCL_1411)


title: Blood, SP vaccine immunized, Day 1，rep1


title: patch-seq sample_S303

description: patchseq.mtx.csv


title: MHHES1, rep3


title: MHHES1, rep1


title: Blood, SP vaccine immunized, pre-immunization (Day 0)，rep1


title: Blood, SP vaccine immunized, pre-immunization (Day 0)，rep2


title: RDES, rep3


title: patch-seq sample_S302

description: patchseq.mtx.csv


title: EW24, rep3


title: Blood, CAD vaccine immunized, Day 1，rep3


title: Blood, vector immunized, Day 1，rep3


title: Blood, vector immunized, Day 1，rep1


title: Blood, vector immunized, Day 1，rep2


title: Blood, vector immunized, pre-immunization (Day 0)，rep3


title: patch-seq sample_S300

description: patchseq.mtx.csv


title: patch-seq sample_S301

description: patchseq.mtx.csv


title: EW24, rep2


title: Blood, vector immunized, pre-immunization (Day 0)，rep2


title: EW24, rep1


title: patch-seq sample_S297

description: patchseq.mtx.csv


title: patch-seq sample_S298

description: patchseq.mtx.csv


title: EW3, rep3

value: EW-3 (RRID:CVCL_1216)


title: EW3, rep2


title: Blood, vector immunized, pre-immunization (Day 0)，rep1


title: RNA JM22-59-8_E8.5_WT_rep2

city: San Francisco

first: Jonathon

middle: M

last: Muncie-Vasic

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description: 10x Genomics Multiome Kit - snRNA-seq library

data_processing:
Libraries were pooled and sequenced on Illumina NovaSeq 6000. Reads were demultiplexed, aligned, read normalized, and quantified using 10X Genomics cellranger-arc-2.0.0 software suite.
Assembly: Reads were mapped to the mm10 reference genome containing an additional sequence for eGFP to map reads of the Smarcd3-F6-eGFP reporter transcript.
Supplementary files format and content: Processed data files consist of the filtered feature matrix files output by running cellranger-arc counts

molecule: nuclear RNA

source_name: embryo

growth_protocol: To achieve timed matings, male and female mice were housed together in the evening and pregnancy was assessed by vaginal plug the following morning. Gestational stage was determined relative to noon on the day of plug detection, defined as day E0.5.

extract_protocol:
Embryos were dissected and, at later stages when yolk was present, also de-yolked, in ice-cold PBS with 1% fetal bovine serum. For E7.75 embryos, whole embryos were dissected and harvested for single-nucleus library generation. For E8.5 and E9 embryos, the head folds and posterior trunk were removed by microdissection prior to harvesting for library generation to enrich the relative capture of cardiac cell types. Rapid PCR genotyping was performed while dissected embryos remained on ice. Embryos selected for the multiome experiment were incubated in 200 μl TrypLE Select for 5 minutes at 37 °C, triturated gently by pipetting up and down, and then incubated an additional 3 minutes at 37 °C. The dissociated cell suspension was quenched with 600 μl of PBS with 1% FBS, singularized by passage through the 35 μm mesh of a 5 mL Falcon™ Round-Bottom Polystyrene Test Tube with Cell Strainer Snap Cap, pelleted by centrifugation at 300 g for 5 minutes at 4 °C, and resuspended in 50 μl of PBS with 0.04% bovine serum albumin (BSA). At this stage, the manufacturer’s protocol for Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing, Appendix, Low Cell Input Nuclei Isolation (10x Genomics, CG000365 Rev B) was followed exactly to prepare nuclei for library generation.
Library construction was performed according to manufacturer's protocols (10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, CG000338 Rev B). Following dissection and rapid genotyping, embryos selected for the multiome experiment were processed directly into the transposition reaction and then captured in 10x Genomics GEMs via the Chromium Controller. GEMs were stored at -80 °C for up to 4 weeks, allowing for collection of replicate embryos of each genotype at each development stage. All subsequent library preparation steps were performed together for all embryos of a given developmental stage to reduce the likelihood of technical batch artifacts. A targeted maximum recovery of 10,000 cells per sample were loaded onto the 10x Genomics Chromium controller instrument. Each sample's snRNA-seq library was indexed with a unique sample identifier with the Dual Index Kit TT Set A (10x Genomics). Final libraries were quality-controlled using an Agilent Bioanlyzer instrument with Agilent High Sensitivity DNA Kit. The DNA concentration of each library was measured using KAPA Library Quantification qPCR Kit.

value: embryo

tag: developmental stage

value: WT


title: RNA JM22-60-3_E8.5_MEF2CKO_rep2

tag: tissue

value: MEF2C KO


title: Blood, SP vaccine immunized, pre-immunization (Day 0)，rep3

tag: treatment


title: RNA JM22-59-2_E8.5_WT_rep1

tag: strain


title: EW3, rep1

tag: cell type


title: patch-seq sample_S296

description: patchseq.mtx.csv

value: cochlear nucleus


title: RNA JM22-59-1_E8.5_MEF2CKO_rep1

tag: genotype


title: RNA JM21-33-6_E9_WT_rep2


title: patch-seq sample_S295

description: patchseq.mtx.csv


title: RNA JM21-30-7_E9_MEF2CKO_rep2


title: A673, rep3

tag: cell line


title: RNA JM21-30-4_E9_WT_rep1


title: RNA JM21-23-8_E7.75_WT_rep2


title: patch-seq sample_S290

description: patchseq.mtx.csv


title: A673, rep2


title: patch-seq sample_S289

description: patchseq.mtx.csv


title: RNA JM21-23-9_E7.75_MEF2CKO_rep1


title: A673, rep1


title: patch-seq sample_S288

description: patchseq.mtx.csv


title: RNA JM21-23-4_E7.75_WT_rep1


title: patch-seq sample_S287

description: patchseq.mtx.csv


title: JM22-59-2_E8.5_WT_rep1

description: 10x Genomics Multiome Kit - snATAC-seq library

library_source: genomic single cell

data_processing:
Libraries were pooled and sequenced on Illumina NovaSeq 6000. Reads were demultiplexed, aligned, read normalized, and quantified using 10X Genomics cellranger-arc-2.0.0 software suite.
Assembly: Reads were mapped to the mm10 reference genome containing an additional sequence for eGFP to map reads of the Smarcd3-F6-eGFP reporter transcript.
Supplementary files format and content: The fragments.tsv.gz files are outputs from the cellranger-arc counts pipeline and consist of BED-like tabular files where each line represents a unique accessible chromatin fragment captured by the assay.
Supplementary files format and content: The fragments.tsv.gz.tbi files are tabix indexes of the fragment intervals, which facilitate random access to records from an arbitrary genomic interval.

extract_protocol:
Embryos were dissected and, at later stages when yolk was present, also de-yolked, in ice-cold PBS with 1% fetal bovine serum. For E7.75 embryos, whole embryos were dissected and harvested for single-nucleus library generation. For E8.5 and E9 embryos, the head folds and posterior trunk were removed by microdissection prior to harvesting for library generation to enrich the relative capture of cardiac cell types. Rapid PCR genotyping was performed while dissected embryos remained on ice. Embryos selected for the multiome experiment were incubated in 200 μl TrypLE Select for 5 minutes at 37 °C, triturated gently by pipetting up and down, and then incubated an additional 3 minutes at 37 °C. The dissociated cell suspension was quenched with 600 μl of PBS with 1% FBS, singularized by passage through the 35 μm mesh of a 5 mL Falcon™ Round-Bottom Polystyrene Test Tube with Cell Strainer Snap Cap, pelleted by centrifugation at 300 g for 5 minutes at 4 °C, and resuspended in 50 μl of PBS with 0.04% bovine serum albumin (BSA). At this stage, the manufacturer’s protocol for Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing, Appendix, Low Cell Input Nuclei Isolation (10x Genomics, CG000365 Rev B) was followed exactly to prepare nuclei for library generation.
Library construction was performed according to manufacturer's protocols (10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, CG000338 Rev B). Following dissection and rapid genotyping, embryos selected for the multiome experiment were processed directly into the transposition reaction and then captured in 10x Genomics GEMs via the Chromium Controller. GEMs were stored at -80 °C for up to 4 weeks, allowing for collection of replicate embryos of each genotype at each development stage. All subsequent library preparation steps were performed together for all embryos of a given developmental stage to reduce the likelihood of technical batch artifacts. A targeted maximum recovery of 10,000 cells per sample were loaded onto the 10x Genomics Chromium controller instrument. Each sample's snATAC-seq library was indexed with a unique sample identifier with the Single Index Kit N Set A (10x Genomics). Final libraries were quality-controlled using an Agilent Bioanlyzer instrument with Agilent High Sensitivity DNA Kit. The DNA concentration of each library was measured using KAPA Library Quantification qPCR Kit.


title: Patient294770_NL_Surgery_LPT

city: Los Angeles

first: Rivkah

last: Gonsky

state: California

address: 8700 Beverly Blvd. Davis Building, Room D4062

department: Gastroenterology/IBIRI

institute: Cedars-Sinai

data_processing:
Expression analysis of CD3+ T cells was performed using Nugen human FFPE RNA-seq library system.
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Reads were mapped to the UCSC transcript set using Bowtie2 version 2.1.0.
DESeq2 (v.1.18.1) was applied to produce normalized counts and the data were log2-transformed
RNA-Seq data analysis and data mining were performed using the BRB array tools
Assembly: hg19

source_name: lamina propria mucosa-derived T cell

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit
total RNA

treatment_protocol: CD3+ T cells were isolated using CD3-immunomagnetic beads (Miltenyi Biotech, Auburn, CA) and were at least 95% pure.

value: lamina propria mucosa-derived T cell

tag: phenotype

value: non-inflammatory bowel disease

value: Surgery


title: JM22-59-8_E8.5_WT_rep2


title: Patient294770_NL_Surgery_PBT

source_name: peripheral blood T cell

value: peripheral blood T cell


title: JM22-60-3_E8.5_MEF2CKO_rep2


title: patch-seq sample_S286

description: patchseq.mtx.csv


title: JM22-59-1_E8.5_MEF2CKO_rep1


title: Patient232737_CD_Surgery_LPT

value: Crohn's disease


title: Patient232737_CD_Surgery_PBT


title: patch-seq sample_S271

description: patchseq.mtx.csv


title: JM21-33-6_E9_WT_rep2


title: patch-seq sample_S269

description: patchseq.mtx.csv


title: JM21-30-5_E9_MEF2CKO_rep1


title: JM21-30-7_E9_MEF2CKO_rep2


title: RNA JM21-30-5_E9_MEF2CKO_rep1


title: Patient294089_CD_Surgery_PBT


title: RNA JM21-23-6_E7.75_MEF2CKO_rep2


title: JM21-23-8_E7.75_WT_rep2


title: Patient294089_CD_Surgery_LPT


title: JM21-30-4_E9_WT_rep1


title: JM21-23-9_E7.75_MEF2CKO_rep1


title: JM21-23-4_E7.75_WT_rep1


title: patch-seq sample_S265

description: patchseq.mtx.csv


title: Patient293411_CD_PostSurgery_PBT

value: PostSurgery


title: patch-seq sample_S267

description: patchseq.mtx.csv


title: Tensile

first: wen

middle: feng

last: shao

address: tonghe

institute: Southern Medical University

data_processing:
GRCm39 release 106 version
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
Assembly: mus musculus GRCm39
Supplementary files format and content: Gene_information xlsx file for each sample

source_name: Synovial membrane

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.

value: Synovial membrane

value: macrophage

value: 20% elongation strain loading for 24 hours


title: NC

value: normal  elongation strain loading for 24 hours


title: patch-seq sample_S266

description: patchseq.mtx.csv


title: Patient293750_CD_Surgery_PBT


title: patch-seq sample_S264

description: patchseq.mtx.csv


title: FSALINE

city: Davis

first: Jessie

last: Muir

address: 1544 Newton Court

department: Center for Neuroscience

institute: UC Davis

description: 10x Genomics 3' v3.1

data_processing:
Analysis was performed using Cell Ranger Software v7.1.0
Assembly: mm10 +scFLARE2 (addgene 158700) + TRE::mCherry-p2a-bReaChES (Addgene 163037)
Supplementary files format and content: Barcode, Features, and Matrix data tables aggregated across all samples
Supplementary files format and content: Excel sheet containing QC data and sample index data used for each file

source_name: Brain; PFC; Expressing scFLARE2 + TRE-mCherry-p2a-bReaChES

extract_protocol:
mPFC of C57BL/J mice were microdissected and frozen on dry ice. Nuclei isolation ws performed using  Chromium Nuclei Isolation with RNase inhibitor Kit (10x Genomics) according to manufacturer's instructions. Briefly, tissue was dissociated with pestle in lysis buffer and incubated on ice in lysis buffer. Dissociated tissue was pipetted into Nuclei Isolation Column and Collection tube and vortexed to resuspend. Supernantant was removed and resultant pellet was resuspended in Debris Removal buffer and vortexed. Supernatant was removed, washed in Resuspension buffer, and vortexed. Nuclei concentration was determined.
Library was constructed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer's instructions. Nuclei and partitioning oil are combined to create Master Mix which is combined with barcoded Gel Beads onto Chromium Next GEM Chip M. The Gel Bead is then dissolved, primers are released, and any copartitioned cell is lysed. Primers containing an Illumina TruSeq Read 1, 16nt 10x Barcode, 12 nt unique molecular identifier (UMI), and 30 nt poly(dT) sequence are mixed with both the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs are broken and pooled fractions are recovered. Silane magnetic beads are used to purify the first-strand cDNA from the post GEMRT reaction mixture, which includes leftover biochemical reagents and primers. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5 and P7 adapters, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.

value: Female

value: 9 weeks

value: Saline


title: MDOI

description: 10x Genomics 3' v3.1

value: Brain; PFC; Expressing scFLARE2 + TRE-mCherry-p2a-bReaChES

value: Male

value: DOI


title: patch-seq sample_S263

description: patchseq.mtx.csv

value: cochlear nucleus


title: MSALINE

description: 10x Genomics 3' v3.1


title: patch-seq sample_S261

description: patchseq.mtx.csv


title: Mouse periosteal cell replicate 2, scRNA-seq

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

description: 10x genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v 6.1.2. (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-choosing-a-pipeline)
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Longbone Periosteum

extract_protocol:
To isolate periosteal cells, the dissected femurs and tibias from C57BL6 WT mice were placed in PBS, and the overlying skin, fascia, and muscle were carefully removed. The bones with periosteum were incubated in ice-cold PBS with 1% FBS for 30min, and the loosely associated periosteum was peeled off using scalpel, forceps, and dissecting scissors. The soft floating periosteal tissues were collected and incubated with 5-10mL of 0.2% collagenase and 10% FBS in PBS at 37ºC for 1 hour and the dissociated periosteal cells were washed with PBS, filtered with a 40um strainer, and resuspended at 1x10^7cells/mL. Isolated cells were FACS-sorted based on CD45, CD31, Ter-119, and DAPI staining. Trypan blue stain was used to assess cell viability and number. Cells were then sorted in 10% FBS with MEM-alpha media.
Libraries were constructed using the Chromium Single Cell 3' v3.1 (10x genomics, PN-11000121) Reagent Kit, according to the manufacturer's protocol. Amplified cDNA and final libraries were evaluated on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies).

value: Longbone Periosteum

value: Periosteal cells

value: WT

value: 4 week old


title: Patient293662_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell

value: Crohn's disease

value: Surgery


title: patch-seq sample_S260

description: patchseq.mtx.csv


title: Patient293784_NL_Surgery_PBT

value: peripheral blood T cell

value: non-inflammatory bowel disease


title: patch-seq sample_S542

description: patchseq.mtx.csv


title: patch-seq sample_S541

description: patchseq.mtx.csv


title: JM21-23-6_E7.75_MEF2CKO_rep2

value: embryo

value: MEF2C KO


title: Patient293784_NL_Surgery_LPT


title: patch-seq sample_S539

description: patchseq.mtx.csv


title: patch-seq sample_S259

description: patchseq.mtx.csv


title: patch-seq sample_S538

description: patchseq.mtx.csv


title: patch-seq sample_S540

description: patchseq.mtx.csv


title: Patient288639_CD_PostSurgery_PBT

value: PostSurgery


title: patch-seq sample_S534

description: patchseq.mtx.csv


title: patch-seq sample_S535

description: patchseq.mtx.csv


title: patch-seq sample_S537

description: patchseq.mtx.csv


title: patch-seq sample_S257

description: patchseq.mtx.csv


title: patch-seq sample_S258

description: patchseq.mtx.csv


title: Patient293750_CD_Surgery_LPT


title: Patient293643_CD_Surgery_PBT


title: Patient293662_CD_Surgery_PBT


title: patch-seq sample_S256

description: patchseq.mtx.csv


title: Mouse periosteal cell replicate 1, scRNA-seq

description: 10x genomics


title: FDOI

description: 10x Genomics 3' v3.1

value: Female

value: 9 weeks


title: patch-seq sample_S254

description: patchseq.mtx.csv


title: patch-seq sample_S531

description: patchseq.mtx.csv


title: patch-seq sample_S533

description: patchseq.mtx.csv


title: patch-seq sample_S530

description: patchseq.mtx.csv


title: patch-seq sample_S529

description: patchseq.mtx.csv


title: patch-seq sample_S253

description: patchseq.mtx.csv


title: patch-seq sample_S527

description: patchseq.mtx.csv


title: patch-seq sample_S528

description: patchseq.mtx.csv


title: Patient293411_CD_Surgery_LPT


title: Patient293411_CD_Surgery_PBT


title: patch-seq sample_S251

description: patchseq.mtx.csv


title: patch-seq sample_S250

description: patchseq.mtx.csv


title: Patient293408_NL_Surgery_PBT


title: patch-seq sample_S526

description: patchseq.mtx.csv


title: Patient293408_NL_Surgery_LPT


title: patch-seq sample_S524

description: patchseq.mtx.csv


title: patch-seq sample_S248

description: patchseq.mtx.csv


title: patch-seq sample_S521

description: patchseq.mtx.csv


title: patch-seq sample_S532

description: patchseq.mtx.csv


title: patch-seq sample_S520

description: patchseq.mtx.csv


title: patch-seq sample_S522

description: patchseq.mtx.csv


title: Patient293643_CD_Surgery_LPT


title: Patient293137_CD_Surgery_PBT


title: patch-seq sample_S519

description: patchseq.mtx.csv


title: patch-seq sample_S517

description: patchseq.mtx.csv


title: patch-seq sample_S245

description: patchseq.mtx.csv


title: patch-seq sample_S244

description: patchseq.mtx.csv


title: Patient288559_CD_PostSurgery_PBT


title: Patient293137_CD_Surgery_LPT


title: patch-seq sample_S516

description: patchseq.mtx.csv


title: patch-seq sample_S246

description: patchseq.mtx.csv


title: patch-seq sample_S518

description: patchseq.mtx.csv


title: patch-seq sample_S243

description: patchseq.mtx.csv


title: patch-seq sample_S515

description: patchseq.mtx.csv


title: Patient288821_CD_Surgery_LPT


title: patch-seq sample_S511

description: patchseq.mtx.csv


title: patch-seq sample_S242

description: patchseq.mtx.csv


title: patch-seq sample_S525

description: patchseq.mtx.csv


title: patch-seq sample_S523

description: patchseq.mtx.csv


title: Patient290765_CD_PostSurgery_PBT


title: patch-seq sample_S510

description: patchseq.mtx.csv


title: patch-seq sample_S507

description: patchseq.mtx.csv


title: patch-seq sample_S509

description: patchseq.mtx.csv


title: Patient293306_NL_Surgery_PBT


title: patch-seq sample_S240

description: patchseq.mtx.csv


title: patch-seq sample_S506

description: patchseq.mtx.csv


title: patch-seq sample_S505

description: patchseq.mtx.csv


title: patch-seq sample_S238

description: patchseq.mtx.csv


title: patch-seq sample_S504

description: patchseq.mtx.csv


title: patch-seq sample_S237

description: patchseq.mtx.csv


title: patch-seq sample_S503

description: patchseq.mtx.csv


title: Patient288821_CD_Surgery_PBT


title: Patient293104_NL_Surgery_PBT


title: Patient293306_NL_Surgery_LPT


title: patch-seq sample_S236

description: patchseq.mtx.csv


title: patch-seq sample_S512

description: patchseq.mtx.csv


title: patch-seq sample_S500

description: patchseq.mtx.csv


title: Patient293104_NL_Surgery_LPT


title: patch-seq sample_S235

description: patchseq.mtx.csv


title: patch-seq sample_S502

description: patchseq.mtx.csv


title: Patient234453_CD_Surgery_PBT


title: patch-seq sample_S501

description: patchseq.mtx.csv


title: patch-seq sample_S234

description: patchseq.mtx.csv


title: patch-seq sample_S498

description: patchseq.mtx.csv


title: patch-seq sample_S497

description: patchseq.mtx.csv


title: patch-seq sample_S232

description: patchseq.mtx.csv


title: Patient234453_CD_Surgery_LPT


title: patch-seq sample_S499

description: patchseq.mtx.csv


title: patch-seq sample_S496

description: patchseq.mtx.csv


title: Patient291751_NL_Surgery_PBT


title: patch-seq sample_S495

description: patchseq.mtx.csv


title: patch-seq sample_S231

description: patchseq.mtx.csv


title: patch-seq sample_S494

description: patchseq.mtx.csv


title: Patient291751_NL_Surgery_LPT


title: patch-seq sample_S492

description: patchseq.mtx.csv


title: patch-seq sample_S490

description: patchseq.mtx.csv


title: Patient284216_CD_Surgery_PBT


title: patch-seq sample_S227

description: patchseq.mtx.csv


title: Patient284216_CD_Surgery_LPT


title: patch-seq sample_S485

description: patchseq.mtx.csv


title: patch-seq sample_S482

description: patchseq.mtx.csv


title: Patient291630_NL_Surgery_PBT


title: patch-seq sample_S486

description: patchseq.mtx.csv


title: patch-seq sample_S481

description: patchseq.mtx.csv


title: patch-seq sample_S225

description: patchseq.mtx.csv


title: patch-seq sample_S224

description: patchseq.mtx.csv


title: patch-seq sample_S477

description: patchseq.mtx.csv


title: patch-seq sample_S476

description: patchseq.mtx.csv


title: patch-seq sample_S480

description: patchseq.mtx.csv


title: patch-seq sample_S474

description: patchseq.mtx.csv


title: patch-seq sample_S493

description: patchseq.mtx.csv


title: patch-seq sample_S223

description: patchseq.mtx.csv


title: Patient291611_NL_Surgery_LPT


title: patch-seq sample_S473

description: patchseq.mtx.csv


title: patch-seq sample_S221

description: patchseq.mtx.csv


title: patch-seq sample_S230

description: patchseq.mtx.csv


title: patch-seq sample_S424

description: patchseq.mtx.csv


title: Patient291630_NL_Surgery_LPT


title: patch-seq sample_S220

description: patchseq.mtx.csv


title: patch-seq sample_S488

description: patchseq.mtx.csv


title: patch-seq sample_S423

description: patchseq.mtx.csv


title: patch-seq sample_S226

description: patchseq.mtx.csv


title: Patient291533_NL_Surgery_PBT


title: patch-seq sample_S422

description: patchseq.mtx.csv


title: patch-seq sample_S420

description: patchseq.mtx.csv


title: patch-seq sample_S219

description: patchseq.mtx.csv


title: patch-seq sample_S417

description: patchseq.mtx.csv


title: patch-seq sample_S479

description: patchseq.mtx.csv


title: Patient291533_NL_Surgery_LPT


title: patch-seq sample_S218

description: patchseq.mtx.csv


title: Patient291611_NL_Surgery_PBT


title: patch-seq sample_S419

description: patchseq.mtx.csv


title: patch-seq sample_S216

description: patchseq.mtx.csv


title: patch-seq sample_S415

description: patchseq.mtx.csv


title: Patient288546_CD_PostSurgery_PBT


title: patch-seq sample_S215

description: patchseq.mtx.csv


title: patch-seq sample_S416

description: patchseq.mtx.csv


title: patch-seq sample_S413

description: patchseq.mtx.csv


title: Patient291515_CD_Surgery_PBT


title: Patient288832_CD_PostSurgery_PBT


title: patch-seq sample_S412

description: patchseq.mtx.csv


title: patch-seq sample_S411

description: patchseq.mtx.csv


title: patch-seq sample_S214

description: patchseq.mtx.csv


title: Patient291515_CD_Surgery_LPT


title: patch-seq sample_S414

description: patchseq.mtx.csv


title: patch-seq sample_S409

description: patchseq.mtx.csv


title: patch-seq sample_S421

description: patchseq.mtx.csv


title: patch-seq sample_S408

description: patchseq.mtx.csv


title: patch-seq sample_S212

description: patchseq.mtx.csv


title: patch-seq sample_S407

description: patchseq.mtx.csv


title: patch-seq sample_S211

description: patchseq.mtx.csv


title: patch-seq sample_S406

description: patchseq.mtx.csv


title: patch-seq sample_S403

description: patchseq.mtx.csv


title: Patient291461_CD_Surgery_PBT


title: patch-seq sample_S402

description: patchseq.mtx.csv


title: patch-seq sample_S401

description: patchseq.mtx.csv


title: patch-seq sample_S209

description: patchseq.mtx.csv


title: Patient291461_CD_Surgery_LPT


title: patch-seq sample_S400

description: patchseq.mtx.csv


title: patch-seq sample_S208

description: patchseq.mtx.csv


title: patch-seq sample_S207

description: patchseq.mtx.csv


title: patch-seq sample_S398

description: patchseq.mtx.csv


title: patch-seq sample_S397

description: patchseq.mtx.csv


title: patch-seq sample_S206

description: patchseq.mtx.csv


title: Patient288810_CD_Surgery_LPT


title: Patient290765_CD_Surgery_PBT


title: patch-seq sample_S395

description: patchseq.mtx.csv


title: patch-seq sample_S399

description: patchseq.mtx.csv


title: patch-seq sample_S393

description: patchseq.mtx.csv


title: patch-seq sample_S394

description: patchseq.mtx.csv


title: Patient235258_CD_Surgery_LPT


title: patch-seq sample_S204

description: patchseq.mtx.csv


title: Patient235258_CD_Surgery_PBT


title: patch-seq sample_S392

description: patchseq.mtx.csv


title: patch-seq sample_S391

description: patchseq.mtx.csv


title: patch-seq sample_S203

description: patchseq.mtx.csv


title: Patient290765_CD_Surgery_LPT


title: patch-seq sample_S390

description: patchseq.mtx.csv


title: patch-seq sample_S205

description: patchseq.mtx.csv


title: patch-seq sample_S405

description: patchseq.mtx.csv


title: patch-seq sample_S389

description: patchseq.mtx.csv


title: patch-seq sample_S202

description: patchseq.mtx.csv


title: patch-seq sample_S388

description: patchseq.mtx.csv


title: Patient288293_CD_PostSurgery_PBT


title: Patient288810_CD_Surgery_PBT


title: Patient288559_CD_Surgery_PBT


title: patch-seq sample_S200

description: patchseq.mtx.csv


title: patch-seq sample_S385

description: patchseq.mtx.csv


title: Patient288559_CD_Surgery_LPT


title: patch-seq sample_S384

description: patchseq.mtx.csv


title: patch-seq sample_S199

description: patchseq.mtx.csv


title: patch-seq sample_S382

description: patchseq.mtx.csv


title: patch-seq sample_S198

description: patchseq.mtx.csv


title: patch-seq sample_S381

description: patchseq.mtx.csv


title: patch-seq sample_S383

description: patchseq.mtx.csv


title: Patient288267_CD_PostSurgery_PBT


title: Patient288051_CD_PostSurgery_PBT


title: Patient290757_NL_Surgery_PBT


title: patch-seq sample_S379

description: patchseq.mtx.csv


title: patch-seq sample_S196

description: patchseq.mtx.csv


title: patch-seq sample_S376

description: patchseq.mtx.csv


title: patch-seq sample_S378

description: patchseq.mtx.csv


title: patch-seq sample_S377

description: patchseq.mtx.csv


title: patch-seq sample_S375

description: patchseq.mtx.csv


title: patch-seq sample_S195

description: patchseq.mtx.csv


title: Patient290757_NL_Surgery_LPT


title: patch-seq sample_S373

description: patchseq.mtx.csv


title: patch-seq sample_S193

description: patchseq.mtx.csv


title: Patient288639_CD_Surgery_PBT


title: patch-seq sample_S372

description: patchseq.mtx.csv


title: patch-seq sample_S386

description: patchseq.mtx.csv


title: Patient288639_CD_Surgery_LPT


title: patch-seq sample_S371

description: patchseq.mtx.csv


title: patch-seq sample_S183

description: patchseq.mtx.csv


title: patch-seq sample_S366

description: patchseq.mtx.csv


title: Patient290612_CD_Surgery_PBT


title: patch-seq sample_S197

description: patchseq.mtx.csv


title: patch-seq sample_S182

description: patchseq.mtx.csv


title: patch-seq sample_S364

description: patchseq.mtx.csv


title: Patient288671_CD_PostSurgery_PBT


title: Patient290612_CD_Surgery_LPT


title: patch-seq sample_S361

description: patchseq.mtx.csv


title: patch-seq sample_S360

description: patchseq.mtx.csv


title: patch-seq sample_S380

description: patchseq.mtx.csv


title: patch-seq sample_S181

description: patchseq.mtx.csv


title: patch-seq sample_S356

description: patchseq.mtx.csv


title: patch-seq sample_S180

description: patchseq.mtx.csv


title: patch-seq sample_S357

description: patchseq.mtx.csv


title: Patient288832_CD_Surgery_LPT


title: patch-seq sample_S355

description: patchseq.mtx.csv


title: patch-seq sample_S179

description: patchseq.mtx.csv


title: Patient288832_CD_Surgery_PBT


title: patch-seq sample_S354

description: patchseq.mtx.csv


title: Patient287793_CD_Surgery_LPT


title: patch-seq sample_S351

description: patchseq.mtx.csv


title: patch-seq sample_S178

description: patchseq.mtx.csv


title: patch-seq sample_S177

description: patchseq.mtx.csv


title: patch-seq sample_S350

description: patchseq.mtx.csv


title: patch-seq sample_S353

description: patchseq.mtx.csv


title: Patient287943_CD_PostSurgery_PBT


title: patch-seq sample_S349

description: patchseq.mtx.csv


title: patch-seq sample_S348

description: patchseq.mtx.csv


title: patch-seq sample_S176

description: patchseq.mtx.csv


title: patch-seq sample_S358

description: patchseq.mtx.csv


title: Patient286261_CD_Surgery_PBT


title: patch-seq sample_S175

description: patchseq.mtx.csv


title: Patient286261_CD_Surgery_LPT


title: patch-seq sample_S345

description: patchseq.mtx.csv


title: patch-seq sample_S347

description: patchseq.mtx.csv


title: patch-seq sample_S346

description: patchseq.mtx.csv


title: patch-seq sample_S344

description: patchseq.mtx.csv


title: patch-seq sample_S172

description: patchseq.mtx.csv


title: Patient287793_CD_Surgery_PBT


title: Patient288596_NL_Surgery_LPT


title: patch-seq sample_S173

description: patchseq.mtx.csv


title: patch-seq sample_S341

description: patchseq.mtx.csv


title: Patient288596_NL_Surgery_PBT


title: patch-seq sample_S352

description: patchseq.mtx.csv


title: patch-seq sample_S171

description: patchseq.mtx.csv


title: patch-seq sample_S343

description: patchseq.mtx.csv


title: patch-seq sample_S342

description: patchseq.mtx.csv


title: Patient288570_NL_Surgery_PBT


title: patch-seq sample_S340

description: patchseq.mtx.csv


title: patch-seq sample_S339

description: patchseq.mtx.csv


title: patch-seq sample_S170

description: patchseq.mtx.csv


title: Patient288570_NL_Surgery_LPT


title: patch-seq sample_S338

description: patchseq.mtx.csv


title: patch-seq sample_S336

description: patchseq.mtx.csv


title: Patient288293_CD_Surgery_PBT


title: patch-seq sample_S168

description: patchseq.mtx.csv


title: patch-seq sample_S335

description: patchseq.mtx.csv


title: patch-seq sample_S334

description: patchseq.mtx.csv


title: patch-seq sample_S333

description: patchseq.mtx.csv


title: patch-seq sample_S337

description: patchseq.mtx.csv


title: patch-seq sample_S169

description: patchseq.mtx.csv


title: Patient288293_CD_Surgery_LPT


title: patch-seq sample_S332

description: patchseq.mtx.csv


title: Patient288555_CD_Surgery_PBT


title: patch-seq sample_S331

description: patchseq.mtx.csv


title: patch-seq sample_S166

description: patchseq.mtx.csv


title: patch-seq sample_S167

description: patchseq.mtx.csv


title: patch-seq sample_S328

description: patchseq.mtx.csv


title: patch-seq sample_S330

description: patchseq.mtx.csv


title: Patient288555_CD_Surgery_LPT


title: patch-seq sample_S327

description: patchseq.mtx.csv


title: Patient288546_CD_Surgery_PBT


title: patch-seq sample_S164

description: patchseq.mtx.csv


title: patch-seq sample_S329

description: patchseq.mtx.csv


title: patch-seq sample_S163

description: patchseq.mtx.csv


title: patch-seq sample_S325

description: patchseq.mtx.csv


title: Patient288546_CD_Surgery_LPT


title: patch-seq sample_S324

description: patchseq.mtx.csv


title: patch-seq sample_S161

description: patchseq.mtx.csv


title: Patient288118_CD_Surgery_PBT


title: patch-seq sample_S326

description: patchseq.mtx.csv


title: patch-seq sample_S323

description: patchseq.mtx.csv


title: patch-seq sample_S320

description: patchseq.mtx.csv


title: Patient288118_CD_Surgery_LPT


title: patch-seq sample_S159

description: patchseq.mtx.csv


title: patch-seq sample_S318

description: patchseq.mtx.csv


title: patch-seq sample_S319

description: patchseq.mtx.csv


title: patch-seq sample_S317

description: patchseq.mtx.csv


title: patch-seq sample_S158

description: patchseq.mtx.csv


title: patch-seq sample_S316

description: patchseq.mtx.csv


title: Patient288434_CD_Surgery_PBT


title: patch-seq sample_S157

description: patchseq.mtx.csv


title: patch-seq sample_S162

description: patchseq.mtx.csv


title: single nucleus sample_p7s1


title: Patient288434_CD_Surgery_LPT


title: single nucleus sample_p6s2


title: patch-seq sample_S156

description: patchseq.mtx.csv


title: Patient288432_NL_Surgery_PBT


title: single nucleus sample_p6s1


title: single nucleus sample_p5s1


title: single nucleus sample_p5s2


title: patch-seq sample_S155

description: patchseq.mtx.csv


title: single nucleus sample_p4s1


title: Patient288432_NL_Surgery_LPT


title: patch-seq sample_S154

description: patchseq.mtx.csv


title: Patient288394_CD_Surgery_PBT


title: BM-pDC, SLC15A4 non-stim, rep4

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
The fastq file was demultiplexed using BRBseq Tools software (version 1.6, Gardeux 2021).
Subsequently, the RNA-seq pipeline was executed on each demultiplexed Fastq file, following these steps: Firstly, reads were subjected to adapter and quality trimming using Cutadapt (version 2.5, Martin 2011). Next, reads corresponding to ribosomal RNA sequences were eliminated using fastq_screen (version 0.11.1, Wingett & Andrews, 2018). The remaining reads underwent further filtering for low complexity with reaper (version 15-065, Davis et al. 2013).
These processed reads were then aligned to the Mus musculus genome (build GRCm38) using STAR (version 2.5.3a, Dobin et al. 2013).
UMI deduplication was performed after the mapping step using UMI-tools dedup functionality (version 0.5.3, Smith et al. 2017).
The count of unique UMIs per gene locus was summarized using htseq-count (version 0.9.1, Anders et al. 2015) with Ensembl 102 gene annotation. The quality of the RNA-seq data alignment was evaluated using RSeQC (version 2.3.7, Wang et al. 2012).
Assembly: build GRCm38
Supplementary files format and content: Tab-delimited text file includes umi counts for each Sample
Library strategy: BRB-seq

source_name: primary cells

growth_protocol: Bone marrow derived plasmacytoid dendritic cells (BM-pDC) were differentiated in IMDM medium supplemented with 10% FBS + antibiotics (penicillin and streptomycin) and was conditioned with 10% of Flt3L containing  media from cell line producing this cytokine. B cells were isolated from spleens by untouched  magnetic separation

extract_protocol:
RNA from BM-pDC was harvested using Qiagen Rneasy Plus Micro kit. RNA from primary splenic B cells was isolated using Zymoresearch Quick-RNA Miniprep kit.
RNA libraries were prepared using BRB-Seq kit from Alithea Genomics, according to the manufacturer's recommendations. A total of 85 ng purified RNA was transferred into the BRB-Seq multiwell plate containing the barcoded oligo-dT primers for the reverse transcription step. All cDNA were pooled into an Eppendorf tube and purified using SPRIselect beads (Beckman) at a 1X ratio. The remaining free primers were digested with an exonuclease step. Second strand synthesis was performed from the purified cDNA pool and cleaned-up with a 0.6X SPRIselect beads step. Double stranded cDNA was then tagmented and purified with a 0.6X SPRIselect beads step. Finally the 3’ terminal fragments were amplified using Unique Dual Indexing (UDI) Illumina adapter primers. After a final 0.7X SPRIselect beads purification step, the library generated was quantified with a fluorimetric method (QubIT, Thermo Scientifics) and its size pattern analyzed with a fragment analyzer (Agilent).

treatment_protocol: Cells were stimulated either with TLR7 agonist (R848 100 ng/ml) or CpG-B (ODN1668 1 uM) for 4 or 6h, respectively

value: primary cells

value: plasmacytoid DC

value: feeble (SLC15A4 deficient)

value: non-stimulated


title: patch-seq sample_S153

description: patchseq.mtx.csv

value: cochlear nucleus


title: Patient284602_CD_PostSurgery_PBT


title: BM-pDC, SLC15A4 TLR7, 4h, rep4


title: BM-pDC, SLC15A4 TLR9, 6h, rep3

value: ODN1668 1uM


title: BM-pDC, SLC15A4 TLR7, 4h, rep3


title: BM-pDC, SLC15A4 TLR9, 6h, rep4


title: BM-pDC, SLC15A4 non-stim, rep3


title: BM-pDC, SLC15A4 TLR9, 6h, rep2


title: patch-seq sample_S149

description: patchseq.mtx.csv


title: Patient233123_CD_Surgery_PBT


title: BM-pDC, SLC15A4 non-stim, rep2


title: BM-pDC, SLC15A4 TLR7, 4h, rep2


title: Patient226867_CD_PostSurgery_PBT


title: patch-seq sample_S148

description: patchseq.mtx.csv


title: Patient233123_CD_Surgery_LPT


title: BM-pDC, SLC15A4 TLR7, 4h, rep1


title: patch-seq sample_S147

description: patchseq.mtx.csv


title: Patient263335_CD_PostSurgery_PBT


title: BM-pDC, TASLDKO TLR9, 6h, rep4

value: TASL, TASL2 double knock-out


title: BM-pDC, SLC15A4 non-stim, rep1


title: patch-seq sample_S146

description: patchseq.mtx.csv


title: BM-pDC, TASLDKO TLR7, 4h, rep4


title: Patient288394_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: BM-pDC, TASLDKO TLR9, 6h, rep3


title: Patient284699_CD_Surgery_LPT

value: Crohn's disease


title: patch-seq sample_S150

description: patchseq.mtx.csv


title: BM-pDC, TASLDKO TLR7, 4h, rep3


title: Patient232836_CD_Surgery_PBT

value: Surgery


title: patch-seq sample_S143

description: patchseq.mtx.csv


title: BM-pDC, TASLDKO non-stim, rep3


title: patch-seq sample_S142

description: patchseq.mtx.csv


title: Patient232836_CD_Surgery_LPT


title: BM-pDC, TASLDKO TLR7, 4h, rep2


title: BM-pDC, TASLDKO non-stim, rep2


title: patch-seq sample_S141

description: patchseq.mtx.csv


title: Patient225217_CD_PostSurgery_PBT

value: peripheral blood T cell


title: BM-pDC, SLC15A4 TLR9, 6h, rep1


title: BM-pDC, TASLDKO TLR7, 4h, rep1


title: patch-seq sample_S140

description: patchseq.mtx.csv


title: BM-pDC, TASLDKO TLR9, 6h, rep1


title: Patient288034_CD_Surgery_PBT


title: BM-pDC, TASL2 TLR9, 6h, rep4

value: TASL2 Knock-out


title: Patient284699_CD_Surgery_PBT


title: BM-pDC, TASLDKO non-stim, rep1


title: patch-seq sample_S139

description: patchseq.mtx.csv


title: patch-seq sample_S145

description: patchseq.mtx.csv


title: Patient288034_CD_Surgery_LPT


title: BM-pDC, TASL2 non-stim, rep4


title: patch-seq sample_S138

description: patchseq.mtx.csv


title: BM-pDC, TASL2 TLR9, 6h, rep3


title: BM-pDC, TASLDKO non-stim, rep4


title: patch-seq sample_S136

description: patchseq.mtx.csv


title: BM-pDC, TASL2 TLR7, 4h, rep3


title: BM-pDC, TASLDKO TLR9, 6h, rep2


title: BM-pDC, TASL2 TLR9, 6h, rep2


title: BM-pDC, TASL2 non-stim, rep3


title: Patient288296_NL_Surgery_LPT

value: non-inflammatory bowel disease


title: BM-pDC, TASL2 TLR7, 4h, rep2


title: Patient288267_CD_Surgery_PBT


title: BM-pDC, TASL2 non-stim, rep2


title: patch-seq sample_S133

description: patchseq.mtx.csv


title: patch-seq sample_S132

description: patchseq.mtx.csv


title: BM-pDC, TASL2 TLR7, 4h, rep1


title: BM-pDC, TASL2 TLR7, 4h, rep4


title: BM-pDC, TASL2 TLR9, 6h, rep1


title: Patient288267_CD_Surgery_LPT


title: BM-pDC, TASL2 non-stim, rep1


title: BM-pDC, TASL TLR9, 6h, rep4

value: TASL Knock-out


title: patch-seq sample_S131

description: patchseq.mtx.csv


title: patch-seq sample_S130

description: patchseq.mtx.csv


title: Patient288296_NL_Surgery_PBT


title: BM-pDC, TASL TLR9, 6h, rep3


title: BM-pDC, TASL non-stim, rep4


title: BM-pDC, TASL TLR7, 4h, rep4


title: patch-seq sample_S129

description: patchseq.mtx.csv


title: Patient288180_NL_Surgery_PBT


title: BM-pDC, TASL non-stim, rep3


title: patch-seq sample_S128

description: patchseq.mtx.csv


title: patch-seq sample_S134

description: patchseq.mtx.csv


title: Patient228750_CD_Surgery_LPT


title: BM-pDC, TASL TLR7, 4h, rep3


title: BM-pDC, TASL TLR9, 6h, rep2


title: Patient288180_NL_Surgery_LPT


title: BM-pDC, TASL non-stim, rep2


title: patch-seq sample_S127

description: patchseq.mtx.csv


title: BM-pDC, TASL TLR7, 4h, rep2


title: Patient288155_NL_Surgery_PBT


title: Patient288155_NL_Surgery_LPT


title: BM-pDC, TASL TLR9, 6h, rep1


title: BM-pDC, TASL TLR7, 4h, rep1


title: patch-seq sample_S126

description: patchseq.mtx.csv


title: Patient239532_CD_PostSurgery_PBT

value: PostSurgery


title: patch-seq sample_S125

description: patchseq.mtx.csv


title: BM-pDC, WT TLR7, 4h, rep4

value: WT


title: Patient283196_CD_Surgery_PBT


title: Patient228750_CD_Surgery_PBT


title: BM-pDC, WT non-stim, rep4


title: Patient283196_CD_Surgery_LPT


title: patch-seq sample_S124

description: patchseq.mtx.csv


title: BM-pDC, WT TLR9, 6h, rep3


title: BM-pDC, WT non-stim, rep3


title: BM-pDC, TASL non-stim, rep1


title: Patient286210_CD_PostSurgery_PBT


title: patch-seq sample_S123

description: patchseq.mtx.csv


title: BM-pDC, WT TLR9, 6h, rep4


title: BM-pDC, WT TLR9, 6h, rep2


title: patch-seq sample_S122

description: patchseq.mtx.csv


title: BM-pDC, WT TLR7, 4h, rep2


title: BM-pDC, WT TLR9, 6h, rep1


title: BM-pDC, WT TLR7, 4h, rep1


title: Patient288051_CD_Surgery_PBT


title: patch-seq sample_S118

description: patchseq.mtx.csv


title: Patient288051_CD_Surgery_LPT


title: B cells, SLC15A4 TLR9, 6h, rep4

value: B cells


title: patch-seq sample_S117

description: patchseq.mtx.csv


title: Patient287943_CD_Surgery_PBT


title: patch-seq sample_S116

description: patchseq.mtx.csv


title: B cells, SLC15A4 TLR9, 6h, rep2

value: primary cells


title: B cells, SLC15A4 non-stim, rep3


title: BM-pDC, WT TLR7, 4h, rep3

value: plasmacytoid DC


title: Patient287943_CD_Surgery_LPT


title: patch-seq sample_S115

description: patchseq.mtx.csv


title: Patient262005_CD_Surgery_PBT


title: patch-seq sample_S114

description: patchseq.mtx.csv


title: B cells, SLC15A4 TLR9, 6h, rep1

value: feeble (SLC15A4 deficient)


title: Patient232836_CD_PostSurgery_PBT


title: B cells, TASLDKO TLR9, 6h, rep4


title: B cells, SLC15A4 non-stim, rep1

value: non-stimulated


title: B cells, TASLDKO non-stim, rep3


title: B cells, TASLDKO TLR9, 6h, rep2


title: Patient262005_CD_Surgery_LPT


title: patch-seq sample_S119

description: patchseq.mtx.csv

value: cochlear nucleus


title: BM-pDC, WT non-stim, rep2


title: B cells, TASLDKO non-stim, rep2


title: Patient287902_NL_Surgery_PBT


title: patch-seq sample_S113

description: patchseq.mtx.csv


title: B cells, TASLDKO TLR9, 6h, rep1

value: ODN1668 1uM


title: Patient287902_NL_Surgery_PBT_Repeat

tag: duplicate

value: Replicate


title: B cells, SLC15A4 TLR9, 6h, rep3


title: BM-pDC, WT non-stim, rep1


title: B cells, TASLDKO TLR9, 6h, rep3

value: TASL, TASL2 double knock-out


title: patch-seq sample_S112

description: patchseq.mtx.csv


title: B cells, TASLDKO non-stim, rep1


title: Patient287902_NL_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: B cells, SLC15A4 non-stim, rep2


title: patch-seq sample_S111

description: patchseq.mtx.csv


title: B cells, TASL2 TLR9, 6h, rep4


title: B cells, TASL2 TLR9, 6h, rep3


title: B cells, TASL2 non-stim, rep3


title: patch-seq sample_S109

description: patchseq.mtx.csv


title: patch-seq sample_S110

description: patchseq.mtx.csv


title: B cells, TASL2 TLR9, 6h, rep2


title: Patient226832_CD_Surgery_LPT

value: Crohn's disease

value: Surgery


title: B cells, TASL2 non-stim, rep2

value: TASL2 Knock-out


title: Patient226832_CD_Surgery_PBT

value: peripheral blood T cell


title: B cells, TASL2 TLR9, 6h, rep1


title: Patient287808_CD_Surgery_PBT


title: B cells, TASL2 non-stim, rep1


title: patch-seq sample_S108

description: patchseq.mtx.csv


title: patch-seq sample_S094

description: patchseq.mtx.csv


title: B cells, TASL TLR9, 6h, rep2

value: TASL Knock-out


title: B cells, TASL TLR9, 6h, rep3


title: B cells, TASL non-stim, rep2


title: B cells, TASL non-stim, rep3


title: patch-seq sample_S106

description: patchseq.mtx.csv


title: patch-seq sample_S107

description: patchseq.mtx.csv


title: Patient287808_CD_Surgery_LPT


title: Patient284790_CD_Surgery_LPT


title: B cells, TASL TLR9, 6h, rep4


title: Patient284790_CD_Surgery_PBT


title: Patient284602_CD_Surgery_PBT


title: B cells, WT TLR9, 6h, rep3


title: B cells, WT TLR9, 6h, rep4


title: B cells, WT TLR9, 6h, rep2


title: B cells, WT non-stim, rep3


title: patch-seq sample_S091

description: patchseq.mtx.csv


title: B cells, WT non-stim, rep2


title: Patient284602_CD_Surgery_LPT


title: patch-seq sample_S090

description: patchseq.mtx.csv


title: Patient286210_CD_Surgery_LPT


title: B cells, WT TLR9, 6h, rep1


title: patch-seq sample_S089

description: patchseq.mtx.csv


title: Patient286210_CD_Surgery_PBT