title: 2015C-CB-F

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Short reads were trimmed usingtrimmomatic(v 0.36), and QC on the original and trimmed reads was performed usingFastQC(v 0.11.4) andMultiQC.
The reads were aligned to the transcriptome usingSTARversion 2.7.9a.
Transcript abundance was quantified usingRSEM(RSEM v1.3.1).
Differential expression analysis was performed usingDESeq2, with an FDR-corrected P-value threshold of 0.05. The output files were further filtered to extract transcripts showing a 2.0-fold change in either direction.
Assembly: Macaca fascicularis 6.0 (ENSEMBL)
Supplementary files format and content: Counts for all transcripts in all samples.

source_name: Grey matter

extract_protocol:
RNA isolation and purification were carried out by the Toxicology Core Facility at the University of Florida. For the temporal lobe, ventral midbrain, and cerebellum, RNA was isolated and prepared for extraction as previously described by Kondratov et. al. Total RNA for each sample was then extracted using a QIAGEN RNeasy® Lipid Tissue kit (Cat #74804) according to the manufacturer's instructions. Each sample’s RNA Integrity Number (RIN) was determined using the Agilent 2100 Bioanalyzer to ensure RIN for each sample was greater than seven.
Post-RNA extraction, a quality-controlled cDNA library was prepared and carried out by the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) in the NextGen DNA Sequencing (NGS) Core facility. Synthesis of cDNA libraries required 50 ng of RNA per sample, and cDNA synthesis reactions were performed using the NEBNext® Strand- switch cDNA synthesis reagents (Cat #E6421). Reactions were first optimized using the RNA samples with the lowest RIN. Amplification reactions were performed using NEBNext® High Fidelity 2X PCR Master Mix (Cat# M0541) at the following conditions: denaturation 98℃ for 45 sec, then cycling 98℃ for 10 sec, 62℃ for 15 sec, 72℃ for 3 min, final extension at 65℃ for 5 min. Each cDNA product underwent quality control using the Invitrogen Qubit® 3.0. Quality control was further ensured by testing every fourth sample using the Agilent 2200 Tape Station; at least 5 Tape Station runs were completed. Libraries were amplified for 14 rounds then sequenced on the Illumina NovaSeq6000. Overall, this generated 1,418,598,125- total reads with percent quality score greater than 30. These same optimized conditions were used to synthesize and amplify double-stranded cDNA for all samples.

value: Grey matter

tag: brain region

value: Cerebellum

value: Female

tag: biorep


title: CB357A-CB-F

status: Public on Nov 01 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Macaca mulatta

tag: tissue

tag: Sex


title: S132

city: Davis

first: Barbara

last: Blanco-Ulate

state: California

address: One Shields Ave

department: Plant Sciences

institute: University of California Davis

description: Rh19- 17 B

data_processing:
Quality and adapter trimming were done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Rhizopus stolonifer and each of the fruit hosts with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the Bowtie2 alignments using the script sam2counts.py v.0.91
Assembly: Rhizopus stolonifer BLUCD01v1, Solanum licopersicum build SL4.0 with ITAG 4.0 annotations, Vitis vinifera PN40024, Fragaria x ananassa Camarosa v1.0.a1, Prunus salicina Zhongli No. 6 v1.0
Supplementary files format and content: Processed data file contains read counts per sample, with each sample being listed on one column from column B-AZ, and transcript IDs being listed on column A
Supplementary files format and content: -

organism: Prunus domestica

source_name: Plum

extract_protocol:
RNA was extracted from 1 g of ground tissue as described in Blanco-Ulate et al. (2013). Culture media-grown samples and resulting libraries were obtained from Petrasch et al. (2019) (GEO accession GSE122555).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

value: Plum

tag: agent

value: Rhizopus stolonifer

tag: time point

value: (hours_post_inoculation)  6


title: S134

description: Rh19-19 B


title: (PPRE)-eGEP-THP-1,M1 differentiation+DMSO,24H,rep2

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

country: China

institute: China National Center for Food Safety Risk Assessment (CFSA)

description:
M1_DMSO2
M1 differentiation+DMSO
Control

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

organism: Homo sapiens

growth_protocol: The THP-1 cell line was maintained in RPMI 1640 complete medium with 10% (vol/vol) FBS and 1% (vol/vol) penicillin/streptomycin. Cells were maintained in an atmosphere of 37°C, 5% carbon dioxide (CO2), and 95% humidity.

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

treatment_protocol: PPRE-eGEP-THP-1 cells were seeded in 6-well plates at 150,0000 cells/well with culture medium containing phorbol 12-myristate 13-acetate (25 ng/mL). After adhesion for 48 h, the cells were allowed to rest in fresh media for 24 h to acquire M0 macrophages. To induce the polarization of M1 or M2 macrophages, M0 macrophages were treated with lipopolysaccharide (LPS; 100 ng/mL) and recombinant human interferon gamma (IFN-γ; 20 ng/mL) or interleukin-4 (IL-4; 20 ng/mL) and IL-13(20 ng/mL), respectively, for 24H. Simultaneously add MCHP (100 μM) during the polarization of M1 or M2 macrophages.

tag: cell line

tag: cell type

value: monocyte

tag: condition

value: M1 polarization of macrophages

tag: treatment

value: DMSO


title: (PPRE)-eGEP-THP-1,M1 differentiation+DMSO,24H,rep3

description:
M1_DMSO3
M1 differentiation+DMSO
Control


title: Sample 4, RRV RLI + TMZ, 5' VDJ immune profiling

city: San Francisco

first: Manish

last: Aghi

state: CA

address: 505 Parnassus Avenue, #M774A

institute: UCSF

description: 10X Genomics

data_processing:
CellRanger v7.0 software using the multi function to produce processed data files for scRNA-seq and TCR-seq.
Assembly: mm10
Assembly: TCR: VDJ GRCm38
Supplementary files format and content: scRNA-seq: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: TCR: filtered_contig_annotations.csv, clonotypes.csv, consensus_annotations.csv
Library strategy: TCR-seq

organism: Mus musculus

source_name: Brain

extract_protocol:
CD45+ leukocytes were isolated from brain tumor tissue of SB28 mice. Four samples corresponding to four different conditions described in the experimental design were analyzed.
Library was constructed per manufacturer's protocol (5' GEX and 5' VDJ immune cell profiling, 10X).

value: Brain

value: CD45+ leukocytes


title: ARNT_fplus macrophages in media 3

city: Little Rock

first: Stephanie

last: Byrum

state: AR

address: 4301 W Markham St, slot 510

department: Dept of Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
read quality was assessed using FastQC (version 0.11.7) and multiQC (version 1.6)
Adaptors, polyA tails, and low-quality bases (Q < 20), and the first 12bp were trimmed using BBTools BBDuk (version 38.52) (minimum read length: 20 base pairs). Parameters: ref=polyA.fa.gz, truseq_rna.fa.gz ktrim=r k=13 useshortkmers=t mink=5 forcetrimleft=12 qtrim=lr trimq=20 minavgquality=20 minlength=20
Trimmed reads were aligned to the mouse reference genome (GRCm38 / mm10) using STAR (version 2.6.1a) allowing up to 2 mismatches depending on the alignment length. Reads mapping to more than 20 locations were discarded. Parameters: --sjdbGTFfile Mus_musculus.GRCm38.84.gtf --outFilterType BySJout --sjdbOverhang 74 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03
Gene level expression counts based on known gene annotation were quantified using HTSeq (htseq-counts) (version 0.9.1) in intersection-nonempty mode. Parameters: --mode intersection-nonempty --stranded yes  --type exon <gff_file> Mus_musculus.GRCm38.84.gtf
A counts-per-million (CPM) filter was applied to remove low abundant genes. Criteria for Retention: Genes with unique Entrez IDs and a minimum of 2 CPM in 4 or more samples.
The filtered counts were TMM normalized and observation-level and sample-specific quality weights calculated using edgeR's (version 3.28.1) calcNormFactors() and limma's (version 3.42.2) voomWithQualityWeights() functions (R version 3.6.3), respectively.
Assembly: GRCm38 / mm10
Supplementary files format and content: tab-delimited text file of gene level counts for each sample

source_name: Ears

growth_protocol: Leishmania major (WHO/MHOM/IL/80/Friedlin) was used. Parasites were maintained in vitro in Schneider's Drosophilia medium supplemented with 20% heat-inactivated FBS, 2mM L-glutamine, 100U/mL penicillin, and 100 mg/ml streptomycin. Metacyclic stationary phase promastigotes were isolated from 4-5 days cultures by Ficoll density gradient seperation. Parasites were used to infect bone marrow-derived macrophages (BMDM) from 2 starins of mice on a C57BL/6 background. Specifically, BMDM were generate from mice that have intact ARNT/HIF-alpha signaling in myeloid cells (LysM Cre ARNT f/+) or mice with deleted ARNT/HIF-alpha signaling in myeloid cells (LysM Cre ARNT f/f). BMDM were generated from mouse bone marrow using L929 supernatants at 25% as a source of MCSF for 7 days. At day 7, BMDM were replated at 1x10^6 cells per well, then incubated overnight in complete DMEM media prior to infection with parasites.

extract_protocol:
The total RNA was isolated from the cell lysate of macrophages under the 3 different conditions by using RNeasy plus mini kit according to the manufacturer's instruction.
cDNA libraries were prepared from total RNA using Lexogen's QuantSeq 3‘ (FWD) mRNA-Seq Library Prep Kit for Illumina following the manufacturer’s protocol. Library fragment sizes were validated using a Fragment Analyzer and quantified by a Qubit fluorometer. Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75bp SE reads per sample.

treatment_protocol: For conditions where macrophages get infected with parasites in vitro, 1x10^6 bone marrow-derived macrophages were infected or not with L. major promastigote parasites (MOI 5:1) in 500 uL DMEM in triplicate. Macrophages were incubated with parasites for 2 hours in culture at 37 degrees. Macrophages were washer 2x to remove extracellular parasites. Next, macrophages were cultured for 8 hours of 3 conditions including: 1) media alone (no infection), 2) L. major infection, or 3) L. major infection plus 100ng/mL LPS plus 10ng/mL of IFNg.

value: Ears

tag: genotype

value: C57BL/6 LysM Cre ARNT f/+


title: BB197D-CB-M

value: Male


title: (PPRE)-eGEP-THP-1,M1 differentiation+DMSO,24H,rep1

description:
M1_DMSO1
M1 differentiation+DMSO
Control


title: ARNT_fplus macrophages in media 2


title: (PPRE)-eGEP-THP-1,M1 differentiation+MCHP,24H,rep3

description:
M1_MCHP3
M1 differentiation+MCHP

value: MCHP


title: ARNT_fplus macrophages in media 1


title: ARNT_fplus macrophages with L. major promastigote parasite infected parasites and LPS/IFNg treatment 3

value: LPS IFNg treated


title: CB367A-CB-M


title: Sample 3, RRV RLI + vehicle, 5' VDJ immune profiling

description: 10X Genomics


title: (PPRE)-eGEP-THP-1,M1 differentiation+MCHP,24H,rep2

description:
M1_MCHP2
M1 differentiation+MCHP


title: Sample 4, RRV RLI + TMZ, scRNA-seq

description: 10X Genomics

data_processing:
CellRanger v7.0 software using the multi function to produce processed data files for scRNA-seq and TCR-seq.
Assembly: mm10
Assembly: TCR: VDJ GRCm38
Supplementary files format and content: scRNA-seq: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: TCR: filtered_contig_annotations.csv, clonotypes.csv, consensus_annotations.csv


title: CB304A-CB-M


title: Parental_Anti-GFP-MRwt ChIP-Seq; 1 hour of 100nM Corticosterone treated cells

city: Bethesda

first: Thomas

middle: A

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

library_source: genomic

data_processing:
Basecalling RTA 3.4.4 was used for Basecalling and Bcl2fastq 2.20 was used for demultiplexing allowing 1 mismatch. Sequences were aligned to the mouse genome (mm10) using Bowtie2 2.3.4.1.  -p 8 -x ref_genome -U read1.fastq (ChIP reads). RNA reads were aligned using STAR 2.7.0f with default settings.
Trimmomatic was used for adapter trimming and quality control.
ChIP-Seq Peaks were called using HOMER program version 4.10.4 with findPeaks with following parameters; FDR<0.001, 5x fold enrichment over control, 5x fold enrichment over local background.
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: bigWig (ChIP-seq) and Excel file of normed counts (RNA-seq)

molecule: genomic DNA

source_name: adenocarcinoma cells

growth_protocol: Cell lines use typical growth protocols with DMEM 10% FBS. Organoids were established in Corning-Matrigel® and IntestiCult®. All cells were grown 24h on media with 10% charcoal stripped serum before hormone treatment.

extract_protocol:
Cells fixed in 1% Formaldehyde. Lysed, Sonicated, and ChIP'd with anti-GFP (10 μg, Abcam #AB290) or anti-GR (10ug Santa Cruz # sc-393232x. Total RNA was collected using Pure-Link RNA Mini kit (Thermo).
ChIP-Seq libraries were made by TruSeq ChIP Library Prep Kit (IP-202-1012). RNA-Seq libraries were made with TruSeq Stranded Total RNA Library Prep.
ChIP-seq was performed with Next-Seq (76bp single-end reads) and RNA-Seq was performed with NOVA-Seq (150bp stranded reads).

treatment_protocol: Aldosterone treatments were with 10 nano-molar. Corticosterone treatments were 100 nano-molar with treatment times as described in the paper.

value: adenocarcinoma cells


title: Parental_Anti-GFP-MRwt ChIP-Seq; 1 hour of 10nM Aldosterone treated cells


title: (PPRE)-eGEP-THP-1,M1 differentiation+MCHP,24H,rep1

description:
M1_MCHP1
M1 differentiation+MCHP


title: BY615B-CB-F

value: Grey matter


title: ARNT_fplus macrophages with L. major promastigote parasite infected parasites and LPS/IFNg treatment 1


title: Nalm6-verteporfin3

city: Fuzhou

first: feng

last: zhang

address: 29 Xinquan Road

institute: Fujian Medical University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) software was used for base calling, and FastQC software was used to evaluate the sequencing quality of the reads after removing adapters (cutadapt was used to remove 3' and 5' adapters).
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software.
Transcript abundance was estimated using StringTie software (1.3.3) with reference to official database annotation information.
The R software Ballgown (v2.10.0) was used to calculate the FPKM at the gene level and the transcript level, and the expression differences at the gene level and the transcript level were calculated respectively, and the differentially expressed genes between samples or groups were screened.
The circRNA is compared to the reference genome by STAR software, Backsplice junction reads detection is performed using CIRCexplorer2, Reads count statistics are performed, and differential expression calculation is performed using R software edgeR.
Assembly: hg18
Supplementary files format and content: The xlsx format file contains the FPKM value of gene in every sample

growth_protocol: NAML6 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Hyclone, UT, USA) 10%FBS(GIMINI,USA).

extract_protocol:
The Nalm6 cells treated by VP and DMSO for 48 hours were washed by phosphate buffer saline,RNA was harvested using Trizol reagent. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: For cell proliferation assays, 1 × 105 NALM6 cells were incubated in verteporfin (VP,0.6mmol/L) (Macklin, Shanghai, China) which dilute with 10%FBS RPMI 1640 medium in 6 wells for 48 hours.

value: verteporfin (VP)


title: 2015C-MB-F

value: Midbrain

value: Female


title: Sample 2, PBS + TMZ, 5' VDJ immune profiling

description: 10X Genomics


title: Parental_Anti-GFP-MRwt ChIP-Seq; 1 hour of vehicle treated cells


title: Nalm6-verteporfin2


title: BY615B-MB-F


title: Sample 2, PBS + TMZ, scRNA-seq

description: 10X Genomics


title: Sample 1, PBS + vehicle 5' VDJ immune profiling

description: 10X Genomics


title: GRKO_Anti-GFP-MRwt ChIP-Seq; 1 hour of 100nM Corticosterone treated cells


title: GRKO_Anti-GFP-MRwt ChIP-Seq; 1 hour of 10nM Aldosterone treated cells


title: CB357A-MB-F


title: Nalm6-verteporfin1


title: Nalm6-DMSO3


title: GRKO_Anti-GFP-MRwt ChIP-Seq; 1 hour of vehicle treated cells


title: Nalm6-DMSO2


title: BB197D-MB-M


title: CB367A-MB-M


title: Sample 1, PBS + vehicle scRNA-seq

description: 10X Genomics


title: Interneurons, IL-13, PND 15, 2 biol rep pooled

first: Ari

last: Molofsky

address: 513 Parnassus Ave

department: Laboratory Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.0.1 (10x Genomics)
Assembly: mm10
Supplementary files format and content: .h5 files

molecule: polyA RNA

source_name: Cortical brain tissue

extract_protocol:
Sensory cortex was dissected from the ipsilateral hemisphere. Tissue was snap frozen on dry ice and stored at -80° Celsius for 1 week. One hemicortex sample from a male and female mouse of the same condition were pooled together for simultaneous nuclei dissociation. RNAse-free instruments and surfaces, tissue was mechanically dissociated using a 2 mL glass tissue homogenizer (Kontes Glassware) on ice using 5 strokes of the loose pestle (A) and 7 strokes of the tight pestle (B) in nuclei isolation media (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris pH 8.0, 0.2 U/uL of Protector RNase inhibitor (Roche), and nuclease free H2O). Dissociated nuclei were pelleted in an Eppendorf tube (1000 g, 5 minutes, 4°C) and gently resuspended in nuclei storage buffer (166.5 mM sucrose, 5 mM MgCl2, 10 mM Tris pH 8.0, 0.2 U/uL of Protector RNase inhibitor and nuclease free H2O) using a P1000 pipette. Nuclei were again pelleted (1000 g, 5 minutes, 4°C) and resuspended in blocking buffer (1% (weight/volume) RNase-free BSA in nuclei storage buffer). Hoechst was added to samples immediately prior to sorting and no immunostaining was performed. Nuclei were sorted on a BD FACSAria Fusion, gated for Hoechst+, single, GFP+ nuclei. Each sorted sample contained 20,000 GFP+ nuclei sorted directly into a 1.5 ml BSA-coated, lubricated Eppendorf tube. No post-sort centrifugation was performed to avoid aggregation and preserve nuclei integrity. The final sort volume was loaded directly into the 10X Genomics Chip.
20,000 sorted nuclei per sample were loaded per well of the Chromium Next GEM Chip G (10X Genomics) and libraries were generated using the Next GEM Single Cell 3’ reagent kit v3.1 (10X Genomics) according to the manufacturer’s instructions.
snRNA-seq

treatment_protocol: Vgat-Cre/+;Sun1-sfGFP/+ mice were injected unilaterally into the lateral ventricle with saline or IL-13 (200 ng) at P15 (1 male and 1 female per condition). Four hours post-injection, mice were perfused with ice cold PBS and brains were dissected on ice.

value: Cortical brain tissue

value: GABAergic neurons

tag: age

value: PND 15


title: Nalm6-DMSO1


title: Gastruloids_Day11

city: Marseille

first: fabienne

last: lescroart

address: 27 bvd Jean Moulin

department: MMG

country: France

institute: Aix-Marseille Univ

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 or v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Gastruloids

extract_protocol:
Gastruloids collected on day 4, 5, 6 and 11 were dissociated by incubation 10 min at 37°c in 0.5% Trypsin-EDTA. Cells were washed 2 times with D-MEM + 10% FBS and filtrated through a 40µm cell strainer. Cell count and viability were determined on a Countess II (Thermo ref AMQAX100).
Single cell-RNA seq libraries were made from 10,000 individual cells using 10X Genomics Chromium Next GEM Single Cell 3’ kit v3.1 (PN-1000268) and the Chromium Controller.

value: Gastruloids

value: mouse embryonic stem cells (mESCs)

value: wild type

tag: developmental stages

value: day 11


title: Sample 3, RRV RLI + vehicle, scRNA-seq

description: 10X Genomics

value: Brain

value: CD45+ leukocytes


title: Interneurons, Saline, PND 15, 2 biol rep pooled

description: 10x Genomics

value: Saline


title: Gastruloids_Day06

description: 10X Genomics

value: day 6


title: BY615B-TL-F

value: Temporal Lobe


title: GM4_crossfostered_sample86

type: genomic

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

description: Genomic DNA isolated from hippocampus of murine mice

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Microarray data was processed using the ENmix version.1.34.02 (Xu et al, 2016) and minfi v.1.44.0 (Aryee et al, 2014packages
Average Beta or normalized (provide the normalization method) Average Beta
Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: Hippocampus

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA was isolated from the hippocampal tissue using the DNeasy Kit (Qiagen, Valencia, CA) following the manufacturer’s instructions.

tag: experimental group

tag: gut microbiota

tag: class

value: crossfostered


title: Gastruloids_Day05

description: 10X Genomics

value: day 5


title: AHH-1 cells, 5 Gy [AHH153]

city: BEIJING

first: XUELEI

last: TIAN

address: 2 Xinkang Street, Deshengmenwai, Beijing

institute: National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention

data_processing:
the quality of raw data from the each group was tested by FastQC software (version 0.11.9)
The qualified raw data were filtered by use of Trimmomatic software (version 0.39) to remove the adaptor and to obtain the clean reads
the reads were mapped to the human reference genome using the STAR software (version 2.7.8a)
DCC software (version 0.5.0) was used to identify the circRNAs and to estimate the circRNA expressions
Differentially expressed circRNAs were identified using the edgeR program (fold change > 1.5, P < 0.05)
Assembly: hg19
Supplementary files format and content: all expressed circRNAs
Supplementary files format and content: differential expressed circRNAs in the 2Gy group compared with the 0Gy group
Supplementary files format and content: differential expressed circRNAs in the 5Gy group compared with the 0Gy group
Supplementary files format and content: all circRNAs reads counts in all groups
Supplementary files format and content: all circRNA CPM values in all groups after TMM normalized

growth_protocol: The cells were maintained in RPMI modified medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. The cells were incubated at 37℃ under saturated humidity with 5% CO2.

extract_protocol:
The total RNA of samples for radiation differential expression circular RNA screening was isolated by TRIzol reagent (Ambion, 15596026) at post-irradiation 4 h.
he libraries were constructed via Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme，China). The size of the libraries was detected by Agilent 2100 Bioanalyzer. And the library’s effective concentrations were accurately determined by Q-PCR (effective concentrations > 3 nM).

treatment_protocol: The exponential growth cells were exposed to 0 (sham irradiation), 2, and 5 Gy 60Co γ-rays at a dose-rate 1 Gy/min at room temperature. The distance from samples to source was 72 cm and the homogeneous irradiated area was 30 cm ×30 cm. A tissue-equivalent chamber was used to calibrate the each exposure step via physical measurements. The calibration uncertainty was 0.1%.

value: B lymphoblastoid cells

value: WT

value: 5 Gy

tag: time

value: 4 h post-irradiation


title: CB367A-TL-M

value: Grey matter

tag: brain region

value: Male


title: GM4_crossfostered_sample85


title: AHH-1 cells, 5 Gy [AHH152]


title: 2015C-TL-F

value: Female

tag: biorep


title: GM4_crossfostered_sample84


title: AHH-1 cells, 5 Gy [AHH151]


title: CB357A-TL-F

tag: tissue


title: GM4_non-crossfostered_sample83

value: non-crossfostered


title: Kidney, rabrhabdomyolysis + CA3

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Assembly: mm10
Supplementary files format and content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

source_name: kidney

extract_protocol:
The single cell suspension with 95% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions
Libraries were sequenced on an Illumina NextSeq500 (Illumina Inc., San Diego, CA).

value: kidney

value: Total cells from mouse kidney

tag: developmental stage

value: 9 weeks

tag: strain

value: rabrhabdomyolysis + CA3


title: Gastruloids_Day04

description: 10X Genomics

value: Gastruloids

value: mouse embryonic stem cells (mESCs)

value: wild type

value: day 4


title: AHH-1 cells, 2 Gy [AHH123]

value: 2 Gy


title: AHH-1 cells, 2 Gy [AHH122]

value: B lymphoblastoid cells


title: Kidney, rabrhabdomyolysis + vehicle

value: rabrhabdomyolysis + vehicle


title: CB304A-MB-M

value: Midbrain

tag: Sex


title: BB197D-TL-M

value: Temporal Lobe


title: GM4_non-crossfostered_sample81


title: Parental_MR-2B12_Ct_GR

data_processing:
Basecalling RTA 3.4.4 was used for Basecalling and Bcl2fastq 2.20 was used for demultiplexing allowing 1 mismatch. Sequences were aligned to the mouse genome (mm10) using Bowtie2 2.3.4.1.  -p 8 -x ref_genome -U read1.fastq (ChIP reads). RNA reads were aligned using STAR 2.7.0f with default settings.
Cutadapt 1.18 was used for adapter trimming and quality control.
ChIP-Seq Peaks were called using HOMER program version 4.10.4 with findPeaks with following parameters; FDR<0.001, 5x fold enrichment over control, 5x fold enrichment over local background.
ChIP-Seq and eRNA heatmaps were made from normalized bigWig files using Deeptools: -of bigwig --binSize 20 --effectiveGenomeSize 2652783500 --normalizeUsing RPGC; computeMatrix reference-point --referencePoint center -S and plot heatmap -m --sortRegions no
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: bigWig (ChIP-seq) and Excel file of normed counts (RNA-seq)

source_name: Parental adenocarcinoma cells

growth_protocol: Typical growth protocols with DMEM 10% FBS. Cells were grown 24h on media with 10% charcoal stripped serum before hormone treatment.

tag: antibody

value: Anti-GR

value: 1 hour of 100nM Corticosterone treated cells


title: CB304A-TL-M

value: Grey matter

value: Male


title: AHH-1 cells, 2 Gy [AHH121]

tag: cell line

tag: cell type

value: WT

value: 4 h post-irradiation


title: GM4_crossfostered_sample75

value: crossfostered


title: AHH-1 cells, control, 0 Gy [AHH103]

tag: treatment

value: 0 Gy


title: Parental_MR-2B12_Ald_GR

value: 1 hour of 10nM Aldosterone treated cells


title: GM4_crossfostered_sample74


title: Parental_MR-2B12_Ct_GFP

value: Anti-GFP


title: AHH-1 cells, control, 0 Gy [AHH102]

tag: genotype


title: GM4_non-crossfostered_sample73

value: non-crossfostered


title: TJ2

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

data_processing:
Illumina Hiseq4000 reads were trimmed using Cutadapt and checked  with FASTQC
Illumina reads were aligned to the Drosophila reference genome (dm6 Ensembl release 70) with Hisat2
Reads normalization, variance estimation and pair-wise differential expression analysis with multiple testing correction were conducted using the R Bioconductor DESeq2 package
Assembly: Drosophila genome (dm6 Ensembl realease 70)
Supplementary files format and content: text file with RNA-seq expression

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
IP against GFP before trizol mRNA extraxtion
Nugen ovation 1-16 droso universal RNAseq kit

value: Ovary

value: somatic lineage

value: tj:gal4, UAS RPL10-GFP


title: Parental_MR-2B12_Ald_GFP


title: AHH-1 cells, control, 0 Gy [AHH101]

value: B lymphoblastoid cells


title: Parental_MR-1G12_NT_GFP

value: 1 hour of vehicle treated cells


title: TJ1


title: GM4_non-crossfostered_sample82


title: GM4_non-crossfostered_sample72


title: F_HCC_FoxM1

city: Xi'an

first: Xunliang

last: Jiang

address: No. 169, Changle West Road, Xincheng District, Xi'an, Shaanxi

institute: Air Force Military Medical University

data_processing:
Chip DNA was end-blunted and added with an "A" base so the adaptors from Illumina with a “T” can ligate on the ends.
Then we used magnetic beads to recover the target size fragments and performed PCR amplification to obtain the library to be sequenced.
The constructed library was checked for quality by agarose electrophoresis. Libraries were quantified using Qubit 2.0 to determine if the library concentration was suitable for use on the machine.
After the library quality inspection was qualified, different libraries were sequenced on the Illumina sequencer according to the requirements of effective concentration and target data volume.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a HiSeq Rapid Duo cBot Sample Loading Kit (Illumina) according to the manufacturer's instructions.
MACS2 (v2.1.1) was used to call peak, giving a robust and high resolution ChIP-Seq peak predictions. Peaks were annotated related genes using Homer (v4.10). ChIPseeker (v1.5.1) was used to depict the reads distribution on chromosomes. Homer (v4.10) was used to search motif and analyze transcription factors.
Assembly: hg38

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA degradation and contamination were monitored on 1% agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The DNA concentration was measured using a Qubit® DNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). A total amount of 50 ng DNA per sample was used as input material for the ChIP sample preparations.
The Chip-Seq library construction mainly includes the steps of cell cross-linking, cell lysis, protein co-immunoprecipitation, extraction of co-precipitated complex DNA, and construction of DNA next-generation sequencing library. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Human hepatocellular carcinoma

tag: chip antibody

value: anti-FoxM1:( Santa Cruz Biotechnology sc-376471)


title: GM4_non-crossfostered_sample71


title: GRKO_MR-2B12_Ct_GFP

source_name: GRKO adenocarcinoma cells

value: 1 hour of 100nM Corticosterone treated cells


title: S3

organism: Rhizopus stolonifer

source_name: Rhizopus stolonifer

value: Rhizopus stolonifer

tag: agent

value: Culture media-grown

tag: time point

value: (hours_post_inoculation)  -


title: GRKO_MR-2B12_Ald_GFP


title: F_HCC_Input

value: IgG


title: S2


title: A_HCC_ASPM

value: anti-ASPM (proteintech; 26223-1-AP)


title: A_HCC_Input


title: GRKO_MR-2B12_NT_GFP


title: Nanos2

value: germline

value: Nos:Gal4Vp16, UAS:RPL10-GFP


title: GM4_crossfostered_sample64

tag: experimental group

tag: gut microbiota

value: crossfostered


title: Nanos1


title: No LDL

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

data_processing:
20 base sgRNA reads were trimmed using Cutadapt 2.3, where 20bp sequence flanked by cgaaacaccg...gttttagagc was identifed from all fastq files
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9
Counts_24-h_AcLDL_2.txt, Counts_24h_OxLDL.txt were edited to delete 78 sgRNA due to contamination of the cDNA library and the edited files are Counts_24h_AcLDL_2_edited.txt, Counts_24h_OxLDL_edited.txt. List of deleted counts Counts_24h_AcLDL_2_deleted.txt, Counts_24h_OxLDL_deleted.txt.
We used MAGeCK Robust Ranking Aggregation (version 0.5.9) algorithm to indentify and rank list of genes significantly enriched by comparing low and high fluorescence population read counts.
Genome_build: Brie_library
Supplementary_files_format_and_content: Comma separated value files for Brie sgRNA library, read counts, and MAGeCK-RRA analysis

source_name: Bone marrow derived macrophage

growth_protocol: BMDM were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.

treatment_protocol: BMDM expressing Cas9 were transduced with the Brie library at a low multiplicity of infection (MOI). Approximately 2.5 x10^7  to 5 x10^7  cells were transduced with 8 x 10^6  or 16 x 10^6  transduction units (TUs) to achieve 200-400-fold representation of each sgRNA. After 48 h, cells were selected with puromycin (5 µg/mL) for two days and were cultured for at least seven more days before the neutral lipid assay and cell sorting. Cells were exposed to AcLDL (50 µg/ml) or OxLDL (100 µg/ml) for 24 h. We scrutinized neutral lipid content in two conditions: 1) 24-h LDL exposure and 2) post LDL 36-48-h. For each condition we treated cells with AcLDL for two replicate populations and treated cells with OxLDL for one replicate for each condition. Before group isolation by fluorescence activated cell sorting BMDMs were stained with 5 µM BODIPY (493/503), a neutral lipid dye, diluted in DMEM for 5 mins, washed once with cold DPBS (-Ca/-Mg) and detached with DPBS (-Ca/-Mg). Next, sorting was done by BD FACs JAZZ cell sorter based on low or high BODIPY fluorescence

value: Primary macrophage

value: 48 hr


title: SC263

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
The genes reads count were computed by RSEM with default settings except choosing STAR 2.7.1a aligner for reads mapping.
The reference transcripts were generated using Hg38 as reference genome and GENCODE v37 as gene annotation
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Head and neck

growth_protocol: SCC154, RTR54, SCC104 and SCC47 were cultured in Minimum Essential Medium (MEM) supplemented with 10% FBS, 1% L-glutamine, and 1% non-essential amino acids. SCC61, RTR61, CAL27, SC263 and FADU were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS and 1% sodium pyruvate.

extract_protocol:
RNA from total cell lysates was isolated using the NucleoSpin RNA kit (Machery Nagel) or RNeasy Mini kit (Qiagen).
Polyadenylated RNA was purified from total RNA using poly-T oligo-attached magnetic beads. The first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Illumina PE150 technology was employed to sequence the samples.

treatment_protocol: No

value: Head and neck

value: Squamous cell

value: WT


title: GM4_crossfostered_sample63

tag: class


title: Lung_ILC2_10x_GEX

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

description:
3'-end gene expression
Hashtag antibodies labeling scRNA-seq

data_processing:
For RNA-seq data: raw fastq files were trimmed with cutadapt v2.10. Alignment to mm10 genome/transcriptome and quantification of gene expression were done using STAR v2.7.5c and RSEM v1.3.3.
For scRNA-seq data: 10x Genomics Cellranger v6.1.1 was used to process fastq files and generate the bam file and matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.0.2.
Assembly: mm10
Supplementary files format and content: tsv, gene expression matrix by cell in the tsv format
Supplementary files format and content: tsv.gz, UMI counts matrix of final ILC2 10x data
Supplementary files format and content: tsv, metadata of final ILC2 10x data
Supplementary files format and content: tsv, umap coordinate of final ILC2 10x data
Supplementary files format and content: tar, 10x hashtag information and library setting
Supplementary files format and content: tar, 10x filtered feature barcode and gene expression matrix files

source_name: Lung

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
For bulk RNA-seq: 2,000 ILC2s from each indicated condition were lysed in 10 μl TCL buffer plus 1% 2-mercaptoethanol. Libraries were processed with SMARTSeq2 with three biological replicates per condition, and paired-end sequenced (150bp × 2).
For scRNA-seq: Flow sorted murine lung ILC2s which were pre-labeled with hashtag antibodies(Biolegend), were pooled and loaded at 60,000 cells per chanel. The cells were then partitioned into the GemCode instrument, where individual cells were lysed and mixed with beads carrying unique barcodes in individual oil droplets. The products were subjected to reverse transcription, emulsion breaking, cDNA amplification, and sample index attachment for paired-end sequencing (150bp × 2).

treatment_protocol: WT mice were intranasally administered dopamine or PBS vehicle in combination with nasal administration of IL-33 for 3 consecutive days, and lung ILC2s were sorted for RNA-seq experiments.

value: Lung

value: wild type

value: male

value: IL-33 plus PBS or dopamine as indicated


title: GM4_non-crossfostered_sample62

value: non-crossfostered


title: Lung_ILC2_SS2_DA3

description:
full-length gene expression
bulk Smart-Seq2

value: female

value: IL-33 plus dopamine


title: Post OxLDL 48h chase: Pre-sort (Pre_LDD3)


title: GM4_non-crossfostered_sample61


title: Cal27


title: SC179


title: Lung_ILC2_SS2_DA2


title: GM4_crossfostered_sample55


title: Post OxLDL 48h chase: Low fluorescent (Low_LDD3)


title: S1

data_processing:
Quality and adapter trimming were done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Rhizopus stolonifer and each of the fruit hosts with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the Bowtie2 alignments using the script sam2counts.py v.0.91
Assembly: Rhizopus stolonifer BLUCD01v1, Solanum licopersicum build SL4.0 with ITAG 4.0 annotations, Vitis vinifera PN40024, Fragaria x ananassa Camarosa v1.0.a1, Prunus salicina Zhongli No. 6 v1.0
Supplementary files format and content: Processed data file contains read counts per sample, with each sample being listed on one column from column B-AZ, and transcript IDs being listed on column A
Supplementary files format and content: -

value: Rhizopus stolonifer

value: Culture media-grown

value: (hours_post_inoculation)  -


title: Lung_ILC2_SS2_DA1


title: GM4_crossfostered_sample65


title: FADU

value: FADU


title: Lung_ILC2_SS2_PBS3

value: IL-33 plus PBS


title: SCC104


title: Post AcLDL 48h chase 2: High fluorescent (High_LDD2)

value: Primary macrophage


title: Post AcLDL 48h chase 2: Pre-sort (Pre_LDD2)

value: 48 hr


title: Post AcLDL 48h chase 2: Input (Input_LDD2)


title: GM4_crossfostered_sample54

value: crossfostered


title: SCC47

value: Head and neck

value: Squamous cell


title: SCC154

value: WT


title: Post AcLDL 48h chase 2: Low fluorescent (Low_LDD2)


title: GM4_non-crossfostered_sample51


title: Lung_ILC2_SS2_PBS2

value: Lung

value: wild type


title: GM4_non-crossfostered_sample52


title: GM4_non-crossfostered_sample53


title: Lung_ILC2_SS2_PBS1


title: Lung_ILC2_10x_hashtag

value: male

value: IL-33 plus PBS or dopamine as indicated


title: Post OxLDL 48h chase: High fluorescent (High_LDD3)


title: Ldlr KO-5

city: Dallas

first: Hasan

last: Zaki

address: 6000 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
RNA sequencing was performed by Novogene (CA).
To ensure the quality of raw RNA sequencing data, initial checks were conducted with FastQC (v0.11.8)
The STAR aligner (v2.7.3a) was used to align the reads to the mm10 reference genome.
Gene expression levels for each sample were quantified using RSEM (v1.3.2) under default settings.
DESeq2 (v1.36.0) was employed to identify differentially expressed genes, with criteria set to an absolute log2 fold change (log2FC) greater than 1 and a false discovery rate (FDR) of 0.01.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: Colon

extract_protocol:
RNA was isolated from mouse colon tissue with trizol reagnt.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Colon

value: DSS


title: SCC090


title: Post AcLDL 48h chase 1: High fluorescent (High LDD1)


title: SCC61


title: GM4_crossfostered_sample44


title: GM1_non-crossfostered_sample43

value: non-crossfostered


title: Ldlr KO-4


title: RTR154-4, rep3

value: RTR154-4 cells


title: Post AcLDL 48h chase 1: Low fluorescent (Low LDD1)


title: Ldlr KO-3


title: 24-h OxLDL: Pre-sort (Pre_LDF3)

value: 24 hr


title: GM1_non-crossfostered_sample42


title: RTR154-4, rep2


title: GM1_crossfostered_sample35


title: GM1_non-crossfostered_sample41


title: Ldlr KO-2


title: RTR154-4, rep1


title: RTR154-1, rep3

value: RTR154-1 cells


title: Ldlr KO-1


title: 24-h OxLDL: Low fluorescent (Low_LDF3)


title: Post AcLDL 48h chase 1: Pre-sort (Pre_LDD1)


title: GM1_crossfostered_sample33


title: 24-h AcLDL 2: Input (Input LDF2)


title: WT-4


title: GM1_crossfostered_sample34


title: RTR154-1, rep2


title: RTR154-1, rep1


title: 24-h AcLDL 2: Pre-sort (Pre_LDF2)


title: RTR154, rep3

value: RTR154 cells


title: WT-3


title: GM1_non-crossfostered_sample32


title: 24-h AcLDL 2: High fluorescent (High LDF2)

value: Primary macrophage


title: GM1_non-crossfostered_sample31


title: RTR154, rep2


title: GM1_crossfostered_sample25


title: GM1_crossfostered_sample24


title: WT-1


title: 24-h OxLDL: High fluorescent (High_LDF3)


title: 24-h AcLDL 1: Input (Input_LDF1)


title: WT-5


title: 24-h AcLDL 1: Pre-sort (Pre_LDF1)


title: GM1_non-crossfostered_sample21


title: SCC154, rep3

value: SCC154 cells


title: GM1_non-crossfostered_sample23


title: 24-h AcLDL 1: Low fluorescent (Low_LDF1)


title: SCC154, rep1


title: GM1_crossfostered_sample15

value: crossfostered


title: Ly6c_Day2_CD40negative_3

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.22.2 R package was utilized to identify differentially expressed genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited text file include sequence read counts of each sample

source_name: liver

extract_protocol:
Isolation of RNA from liver was performed using NucleoSpin RNA Kit from Macherey-Nagel.
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

value: liver

tag: age

value: 7 weeks

value: Ly6C CD40 neg

tag: day


title: WT-2

tag: tissue


title: RTR61-4, rep3

value: Head and neck

value: RTR61-4 cells

value: Squamous cell

value: WT


title: RTR61-4, rep2


title: Ly6c_Day2_CD40negative_4


title: 24-h AcLDL 2: Low fluorescent (Low LDF2)


title: GM1_crossfostered_sample14


title: GM1_non-crossfostered_sample12


title: Ly6c_Day2_CD40negative_2


title: GM1_crossfostered_sample13


title: RTR61-4, rep1


title: RTR61-1, rep3

value: RTR61-1 cells


title: Ly6c_Day2_CD40negative_1


title: RTR61-1, rep2


title: RTR154, rep1


title: GM1_non-crossfostered_sample11


title: GM1_non-crossfostered_sample22


title: SCC154, rep2


title: CD40_Day2_4


title: 24-h AcLDL 1: High fluorescent (High_LDF1)


title: RTR61-1, rep1


title: GM4_Dam_sample8

value: dam


title: GM4_Dam_sample6


title: CD40_Day2_3


title: GM4_Dam_sample5


title: RTR61, rep2

value: RTR61 cells


title: CD40_Day2_2


title: RTR61, rep3


title: GM1_Dam_sample4


title: RTR61, rep1


title: SCC61, rep3

value: SCC61 cells


title: Kupffer-CellsDay7_2

value: Kupffer cells


title: GM4_Dam_sample7


title: Kupffer-CellsDay7_1


title: CD40_Day2_1


title: Kupffer-CellsDay0_2


title: GM1_Dam_sample3


title: SCC61, rep1


title: Kupffer-CellsDay0_1


title: GM1_Dam_sample2


title: RTR61 cells, cytoplasmic RNA, siSNHG6, rep3

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS and 1% sodium pyruvate.

extract_protocol:
RNA from total cell lysates was isolated using the NucleoSpin RNA kit (Machery Nagel) or RNeasy Mini kit (Qiagen). Cytoplasmic fractionation was done using the NucleiEZ nuclei isolation kit (Sigma-Aldrich), and RNA was then purified using Trizol (Invitrogen) according to the manufacturer’s protocol.
Polyadenylated RNA was purified from total RNA using poly-T oligo-attached magnetic beads. The first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. Illumina PE150 technology was employed to sequence the samples.

value: SNHG6 knockdown


title: HUVECs, AngII+Ad-METTL3_2, IP

first: xiaoxiao

last: Yang

state: Tianjin

address: 22 Qixiangtai Road, Heping District

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38). Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using Hisat2 (v2.2.1). After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 1.8.0). HOMER software (v4.1.1) was used to de novo identify consensus motifs from the enriched m9A modification sites. For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using exomepeak software and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
GRCh38
tab-delimited text files include fold changes and p values

source_name: HUVECs

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2107 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8548) following the manufacturer’s instructions.

value: HUVECs

value: Human umbilical vein endothelial cells

value: Treated by Ang II with adenovirus overexpression of METTL3

value: m6A antibody (Synaptic Systems)


title: GM1_Dam_sample1


title: RTR61 cells, cytoplasmic RNA, siSNHG6, rep2


title: HUVECs, AngII+Ad-METTL3_1, IP

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38). Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using Hisat2 (v2.2.1). After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 1.8.0). HOMER software (v4.1.1) was used to de novo identify consensus motifs from the enriched m8A modification sites. For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using exomepeak software and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
GRCh38
tab-delimited text files include fold changes and p values

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2106 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8547) following the manufacturer’s instructions.


title: RTR61 cells, cytoplasmic RNA, siSNHG6, rep1


title: HUVECs, AngII_1, IP

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38). Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using Hisat2 (v2.2.1). After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 1.8.0). HOMER software (v4.1.1) was used to de novo identify consensus motifs from the enriched m6A modification sites. For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using exomepeak software and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
GRCh38
tab-delimited text files include fold changes and p values

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2104 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8545) following the manufacturer’s instructions.

value: Treated by Ang II without adenovirus overexpression of METTL3


title: RTR61 cells, cytoplasmic RNA, siScramble, rep2


title: HUVECs, AngII+Ad-METTL3_2, Input

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38). Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using hisat2 (v2.2.1). Read count extraction were performed using the featureCounts function included in the Rsubread (v2.4.3).
GRCh38
tab-delimited text files includes raw counts for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2103 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8544) following the manufacturer’s instructions.


title: SCC61, rep2


title: HUVECs, AngII+Ad-METTL3_1, Input

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2102 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8543) following the manufacturer’s instructions.


title: KD-rep3

type: RNA

city: Wuhu

first: xiao

middle: long

last: zhu

state: Anhui

address: 2 Zheshan western road

institute: Yijishan Hospital

description: Gene expression data from U251-shCPVL

hyb_protocol: Following fragmentation, aRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

label_protocol: Biotinylated aRNA were prepared according to the GeneChip 3’IVT Express Kit protocol.

growth_protocol: For lentiviral shRNA transfection, U251 cells were seeded in six-well plates (10000 cells/well) and transfected with negative control (NC) shRNA or CPVL-specific lentiviral shRNA when the cell density reached 30–50% confluence according to the manufacturer’s instructions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: KD-rep1

description: Gene expression data from U251-shCPVL


title: RTR61 cells, cytoplasmic RNA, siScramble, rep1


title: KD-rep2

description: Gene expression data from U251-shCPVL


title: NC-rep3

description: Gene expression data from U251-shCtrl


title: NC-rep2

description: Gene expression data from U251-shCtrl


title: NC-rep1

description: Gene expression data from U251-shCtrl


title: HUVECs, AngII_2, Input

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2101 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8542) following the manufacturer’s instructions.


title: RTR61 cells, total RNA, siSNHG6, rep3


title: RTR61 cells, total RNA, siSNHG6, rep2


title: HUVECs, AngII_1, Input

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2100 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8541) following the manufacturer’s instructions.


title: RTR61 cells, total RNA, siSNHG6, rep1


title: Day15-SW620

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

description: Single Cell RNA

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 4.0).
First, Illumina BCL files were de-multiplexed and converted to FASTQs using mkfastq.
Second, FASTQs were then used to quantify gene expression using Cell Ranger count and the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference.
Lastly, cellranger aggr took outputs from multiple runs of cellranger count, and normalized these runs to the same sequencing depth and recomputed the gene-barcode matrices and analysis on the combined data .
Genome_build: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary_files_format_and_content: gene expression counts in 10X format (separate barcodes, features, and matrix files for each sample).

source_name: Human colorectal cancer cell

growth_protocol: SW620 and SW620-TET2CD were cultured for 15 days without passage.

extract_protocol:
Cells was harvested following 10x Genomics® Single Cell Protocols.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1(Cat# PN-100012) was used for the construction of sequencing libraries.

value: colorectal cancer


title: Day15-SW620-TET2CD

description: Single Cell RNA


title: RTR61 cells, total RNA, siScramble,rep3


title: RTR61 cells, cytoplasmic RNA, siScramble, rep3


title: HUVECs, AngII_2, IP

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38). Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using Hisat2 (v2.2.1). After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 1.8.0). HOMER software (v4.1.1) was used to de novo identify consensus motifs from the enriched m7A modification sites. For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using exomepeak software and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
GRCh38
tab-delimited text files include fold changes and p values

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2105 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8546) following the manufacturer’s instructions.


title: DKO ABA REPLICATE 2

city: New Delhi

first: Amrapali

last: Sharma

state: Delhi

address: Benito Juarez road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression analysis from one week old seedlings

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: The raw data (CEL) files were analyzed using GeneSpring GX software (p value ≥ 0.05). We have used RMA algorithm for normalization.

label: Biotin

organism: Arabidopsis thaliana

source_name: 1 week old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each genotype were surface sterilized with 70% ethanol followed by 2 % sodium hypochloride with repeated rinses with dd-water, and were grown in 1/2MS media for seven days.

extract_protocol: Total RNA extraction from whole seedlings was performed according to the manufacturer's instructions using the Qiagen RNeasy Plant mini kit.

treatment_protocol: Seedlings were grown on 1/2 MS medium or 1/2 MS+ ABA medium

value: mbd1 pyl5 double knock out

tag: ecotype

value: 1/2 MS + ABA


title: RTR61 cells, total RNA, siScramble,rep2

value: Head and neck


title: DKO MS REPLICATE 2


title: DKO MS REPLICATE 1


title: PYL5 MS REPLICATE 2

value: pyl5 knockout


title: PYL5 ABA REPLICATE 2


title: PYL5 ABA REPLICATE 1


title: DKO ABA REPLICATE1


title: Day12-SW620-TET2CD

description: Single Cell RNA


title: Day12-SW620

description: Single Cell RNA


title: RTR61 cells, total RNA, siScramble,rep1

value: Squamous cell

value: WT


title: Day9-SW620-TET2CD

description: Single Cell RNA


title: ovary,MCA205_VAC_1

city: Hefei

first: 丛蓉

last: 李

address: 安徽医科大学东校区弘毅楼1202室

institute: Nanjing Medical university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36)
low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Homo sapiens  using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: mm10
Supplementary files format and content: tab-delimited textefile includes raw counts for each sample
Supplementary files format and content: tab-delimited textefile includes RPKM values for each sample

source_name: ovary

extract_protocol:
Total RNAs were extracted from ovaries using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: ovary

value: female


title: PYL5 MS REPLICATE 1


title: SCC61 cells, rep3

data_processing:
The 3’ adaptor sequence (TGGAATTCTCGGGTGCCAAGG) was trimmed from the RiboSeq reads using the cutadapt 3.2 with parameters (-j 10 -m 20 --discard-untrimmed).
To filter contamination, rRNA-derived reads were identified and removed by bowtie version 2.3.4.1 with default settings.
The cleaned reads were aligned to human genome Hg38 using the STAR v 2.7.0 3 with parameters (--outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMatchNmin 16  --outSAMtype BAM SortedByCoordinate  --quantMode TranscriptomeSAM  --alignEndsType EndToEnd  --outFilterMismatchNmax 0).
The RiboCode package was used to identify ORFs.
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes the information of all predicted ORFs in each transcript
Library strategy: Ribo-seq

extract_protocol:
The total RNA from 2 μg of the lysate was purified with the RNA Clean and Concentrator-5 kit (Zymo Research). 15 μg of lysate was digested with RNase I (Thermofisher) at 21°C for 45 min. The digested lysate was purified on a MicroSpin S-400 HR Sephacryl column (GE Healthcare). Ribosome-protected fragments (RPFs) of 28-30 nt were selected by loading the footprints on a Novex TBE-Urea gel (15%) (Thermofisher) and performing gel electrophoresis. The gel parts corresponding to the fragments of interest were excised and let to diffuse in molecular grade water supplemented with ammonium acetate and SDS overnight at 4°C.
The Small RNA Library prep kit (Lexogen) was used to generate the library.
Ribo-seq; High coverage sequencing was performed on the Illumina NovaSeq6000, SE50 single index configuration.

value: SCC61 cells


title: SCC61 cells, rep2


title: Day9-SW620

description: Single Cell RNA


title: ovary,MCA205_PD1_3

address: 安徽医科大学东校区弘毅楼1202室


title: MBD1 ABA REPLICATE 3

value: mbd1 knockout


title: Day6-SW620-TET2CD

description: Single Cell RNA


title: MBD1 ABA REPLICATE 2


title: MBD1 ABA REPLICATE 1


title: SCC61 cells, rep1


title: ovary,MCA205_PD1_1

address: 安徽医科大学东校区弘毅楼1202室


title: RTR61 cells, rep3

value: RTR61 cells


title: ovary,MCA205_3

address: 安徽医科大学东校区弘毅楼1202室


title: Day6-SW620

description: Single Cell RNA


title: RTR61 cells, rep2


title: ovary,MCA205_VAC_2

address: 安徽医科大学东校区弘毅楼1202室


title: ovary,MCA205_2

address: 安徽医科大学东校区弘毅楼1202室


title: ovary,MCA205_VAC_3

address: 安徽医科大学东校区弘毅楼1202室


title: Rrp40G11A, replicate 2, snRNAseq

city: Los Angeles

first: Lauryn

middle: Alexis

last: Higginson

address: 1050 Childs Way Room 201B

department: Biological Sciences

institute: University of Southern California

description: 10X Genomics

data_processing:
The reads were mapped to BDGP D. melanogaster (r6.25) genome. Cell ranger (10X Genomics) was used to create the reference.
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: head

extract_protocol:
Two biological replicates of newly eclosed adult female flies were prepared for each biological replicate (Rrp40WT, Rrp40G11A, and Rrp40G146C). For each sample, 20 fly heads were pooled together, and nuclei were dissociated using the methods adopted from (McLaughlin et al., 2022; Teefy et al., 2022). For the nuclei dissociation, nuclei were dissociated in 1000µL of homogenization buffer (nuclease free water, sucrose, 10mM Tris (pH 8.0), 25 mM KCl, 5 mM MgCl2, 0.1% Triton-x 100, RNasin Plus, 1x protease inhibitor, and 0.1mM DTT) with a 1mL Dounce homogenizer. Homogenization was performed on ice with 20 passes of the loose Dounce and 40 passes of the tight Dounce pestle, and then filtered the solution with a 70µm cell filter into a 15mL conical precoated in 5% Bovine serum albumin. 4mL of nuclei wash buffer (0.5% BSA, PBS, and RNasin Plus) was added to the sample over the filter. Sample was centrifuged, and supernatant was discarded. Another wash step was performed with 5 mL of wash buffer and centrifuged again. Discard the supernatant, resuspend the pellet with 1mL of wash buffer, then transfer to a FACS tube. Add 600µL of debris removal solution (Miltenyi Biotec, Cat# 30-109-398), then 2mL of the resuspension buffer (0.5% BSA, PBS, RNasin) slowly on top. Samples were centrifuged and washed again as described above. Following supernatant removal, the nuclei were resuspended in 150µL of resuspension buffer using a wide-bore tip. The sample was then drawn with a standard pipette and filtered once more using a 40µm Flowmi strainer.
Single-cell libraries were prepared using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN- 1000213) according to manufacturer’s instructions (10x Genomics User Guide Chromium Next GEM Single-cell 30 Reagent Kits v3.1 (CG000204, Rev D)).

value: head

value: Day 1 Adult


title: MBD1 MS REPLICATE 3


title: RTR61 cells, rep1


title: ovary,MCA205_PD1_2

address: 安徽医科大学东校区弘毅楼1202室


title: Rrp40G146C, replicate 2, snRNAseq

description: 10X Genomics


title: Rrp40G11A, replicate 1, snRNAseq

description: 10X Genomics


title: ovary ,Control _2

address: 安徽医科大学东校区弘毅楼1202室

value: Control


title: MBD1 MS REPLICATE 1


title: MBD1 MS REPLICATE 2


title: ovary ,Control _3

address: 安徽医科大学东校区弘毅楼1202室


title: EV_2_Input

city: nanjing

first: zhou

middle: yan

last: yan

address: xianlin road

institute: nanjing univercity of China medicine

data_processing:
Fastp 0.19.11 software performs basic quality statistics for raw reads
QC analysis was used by  fastqc v0.11.5
burrows Wheeler aligner(0.7.12-r1039) can  compare reads to reference genome
Peak calling was performed by MACS22.1.0
The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1)
Genome_build: GRCh38

source_name: Multiple Myeloma cells

growth_protocol: Human multiple myeloma cell lines CAG were cultured in RPMI 1640 Medium  with 10% fetal bovine serum 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured in a humidified atmosphere of 5 % CO2 at 37℃.

extract_protocol:
~5-20 × 106 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of FLAG and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using a phenol-chloroform lysate to obtain a purified product.
RNA samples were fragmented by RNA fragmentation buffer (10 mM Tris-HCl [pH 7.0], 10 mM ZnCl2). Fragmented RNA was incubated for 2 hr at 4C with 0.5 mg/mL antim6A polyclonal antibody in IP buffer (150 mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl [pH 7.4]) supplemented with RNasin Plus RNase inhibitor (Promega). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H - ）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Illumina HiSeqTM 2500 system.

value: Multiple Myeloma

tag: genotype/variation

value: empty vector

value: CAG

value: input


title: WT ABA REPLICATE 2

value: Wild-type

value: 1/2 MS + ABA


title: ovary,MCA205_1

address: 安徽医科大学东校区弘毅楼1202室

tag: Sex


title: Rrp40WT, replicate 2, snRNAseq

description: 10X Genomics


title: OE_2_IP

value: DAZAP1 OE

value: IP


title: Rrp40WT, replicate 1, snRNAseq

description: 10X Genomics

value: WT


title: WT ABA REPLICATE 3


title: OE_2_Input


title: EV_2_IP


title: ATAC-seq for CD8-TCR-noStimulation Experiment-Replicate 3

status: Public on Oct 31 2024

city: Beijing

first: Xin

last: Lin

state: Beijng

address: chengfu road, Haidian

institute: Tsinghua University

data_processing:
ATAC-seq: Raw fastq reads were trimmed to remove the Nextera sequencing adaptors using trim_galore. The trimmed reads were mapped to the mouse reference (hg38) genome using BWA. Reads with a mapping quality of <30 and duplications were removed using SAMtools. Motif enrichment scores were analyzed by chromVAR (Schep et al., 2017). RNA-seq: The adaptors of paired-end reads were trimmed and quality control checks were carried out using trim-galore. Reads were aligned to human genome reference from GENCODE using HISAT2. Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools with parameter is ‘samtools view –b –h –F 4 –f 3’. featureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from GENCODE. Differential gene expression analysis was conducted, which used raw counts as input using R package DESeq2
Assembly: Hg38
Supplementary files format and content: bw and counts files

source_name: CD8 T cells

extract_protocol:
ATAC-seq: Nuclei of 50,000 T cells were isolated according to the Omni-ATAC protocol (Corces et al., 2017). The cell pellet was lysed with 0.1 ml Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin (G9441; Promega), 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl (pH 7.4) for 3 min on ice. Then, 1 ml wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% bovine serum albumin (130-091-376; Miltenyi Biotec) and 0.1% Tween-20) was added to the lysed cells. Nuclei were spun down for 5 min at 500g and 4 °C and resuspended in 50 μL wash buffer.  RNA-seq: RNA-seq library preparation was performed using Smart-seq2 (Picelli et al., 2014) as described with modification allowing higher quality library generation. Briefly, 1,000 sorted T cells were directly sorted into 8 μl RLT lysis buffer and 1% (vol/vol) 2-mercaptoethanol.
ATAC-seq: .The isolated nuclei were combined with 5 µl 10 mM MgCl2, 10 µl 5× TTBL, 5 µl Tn5 transposome (TD501; Vazyme) and 20 µl H2O to form a transposition mix, which was then incubated for 60 min at 37 °C with gentle shaking at 500 r.p.m.  The reactions were cleaned up with the DNA Clean & Concentrator kit (D4014; Zymo Research) and eluted in 21 µl H2O. For PCR reactions, each well was mixed with 2.5 μl 10 μM N5 index primer (AATGATACGGCGACCACCGAGATCTACAC (8-bp barcode) TCGTCGGCAGCGTC), 2.5 µl 10 μM N7 index primer (CAAGCAGAAGACGGCATACGAGAT (8-bp barcode) GTCTCGTGGGCTCGG) and 25 µl NEBNext High-Fidelity 2X PCR Master Mix (M0541L; New England Biolabs). Amplification was carried out using the following thermocycling program: 72 °C for 5 min; 98 °C for 30 s; nine cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; and a final 72 °C for 5 min. Afterwards, the amplified libraries were purified using 1.2× SPRIselect Beads (A63881; Beckman Coulter) and quantified by Qubit 3.0 Fluorometer (Q33216; Thermo Fisher Scientific). The size ranges of the PCR products were assessed using an Agilent 4200 Bioanalyzer. All libraries were sequenced with paired-end 150-bp reads on the illumina Novaseq platform. RNA-seq: RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2×) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.

value: CD8 T cells

value: TCR-noStimulation


title: ATAC-seq for CD8-TCR-noStimulation Experiment-Replicate 2


title: ATAC-seq for CD8-TCR-noStimulation Experiment-Replicate 1


title: ATAC-seq for CD8-TCR-1uM Experiment-Replicate 3


title: ATAC-seq for CD8-TCR-1uM Experiment-Replicate 1


title: ATAC-seq for CD8-TCR-10nM Experiment-Replicate 3


title: ovary ,Control _1

address: 安徽医科大学东校区弘毅楼1202室

value: ovary

value: female


title: ATAC-seq for CD8-TCR-1uM Experiment-Replicate 2


title: WT MS REPLICATE 2


title: Rrp40G146C, replicate 1, snRNAseq

description: 10X Genomics


title: ATAC-seq for CD8-TCR-10nM Experiment-Replicate 2


title: WT MS REPLICATE 3


title: ATAC-seq for CD8-TCR-10nM Experiment-Replicate 1


title: ATAC-seq for CD8-TCR-100nM Experiment-Replicate 2


title: ATAC-seq for CD8-TCR-100nM Experiment-Replicate 1


title: ATAC-seq for CD8-TCR-100nM Experiment-Replicate 3


title: ATAC-seq for CD8-STAR-noStimulation Experiment-Replicate 1

value: STAR-noStimulation


title: ATAC-seq for CD8-STAR-noStimulation Experiment-Replicate 3


title: ATAC-seq for CD8-STAR-noStimulation Experiment-Replicate 2


title: WT MS REPLICATE 1


title: WT ABA REPLICATE 1


title: ATAC-seq for CD8-STAR-1uM Experiment-Replicate 3


title: ATAC-seq for CD8-STAR-1uM Experiment-Replicate 1


title: ATAC-seq for CD8-STAR-10nM Experiment-Replicate 3


title: ATAC-seq for CD8-STAR-10nM Experiment-Replicate 1


title: ATAC-seq for CD8-STAR-10nM Experiment-Replicate 2


title: ATAC-seq for CD8-STAR-100nM Experiment-Replicate 3


title: ATAC-seq for CD8-STAR-100nM Experiment-Replicate 2


title: ATAC-seq for CD8-STAR-100nM Experiment-Replicate 1


title: ATAC-seq for CD8-28zCAR-noStimulation Experiment-Replicate 2


title: ATAC-seq for CD8-28zCAR-1uM Experiment-Replicate 1


title: ATAC-seq for CD8-28zCAR-1uM Experiment-Replicate 2


title: ATAC-seq for CD8-28zCAR-10nM Experiment-Replicate 1


title: ATAC-seq for CD8-28zCAR-10nM Experiment-Replicate 3


title: ATAC-seq for CD8-28zCAR-10nM Experiment-Replicate 2


title: ATAC-seq for CD8-28zCAR-1uM Experiment-Replicate 3


title: ATAC-seq for CD8-28zCAR-noStimulation Experiment-Replicate 1


title: ATAC-seq for CD8-28zCAR-100nM Experiment-Replicate 2


title: ATAC-seq for CD8-28zCAR-100nM Experiment-Replicate 3


title: ATAC-seq for CD4-TCR-1uM Experiment-Replicate 3

source_name: CD4 T cells

value: CD4 T cells


title: ATAC-seq for CD4-TCR-noStimulation Experiment-Replicate 1


title: ATAC-seq for CD4-TCR-10nM Experiment-Replicate 3


title: ATAC-seq for CD4-TCR-1uM Experiment-Replicate 1


title: ATAC-seq for CD8-STAR-1uM Experiment-Replicate 2


title: ATAC-seq for CD4-TCR-1uM Experiment-Replicate 2


title: ATAC-seq for CD4-TCR-noStimulation Experiment-Replicate 3


title: ATAC-seq for CD4-TCR-10nM Experiment-Replicate 2


title: ATAC-seq for CD4-TCR-100nM Experiment-Replicate 2


title: ATAC-seq for CD4-TCR-100nM Experiment-Replicate 3


title: ATAC-seq for CD4-STAR-noStimulation Experiment-Replicate 3


title: ATAC-seq for CD8-28zCAR-noStimulation Experiment-Replicate 3


title: ATAC-seq for CD4-TCR-100nM Experiment-Replicate 1


title: ATAC-seq for CD4-STAR-noStimulation Experiment-Replicate 2


title: ATAC-seq for CD4-STAR-1uM Experiment-Replicate 3


title: ATAC-seq for CD4-STAR-1uM Experiment-Replicate 1


title: ATAC-seq for CD4-TCR-10nM Experiment-Replicate 1


title: ATAC-seq for CD8-28zCAR-100nM Experiment-Replicate 1


title: ATAC-seq for CD4-STAR-10nM Experiment-Replicate 3


title: ATAC-seq for CD4-STAR-10nM Experiment-Replicate 1


title: ATAC-seq for CD4-STAR-1uM Experiment-Replicate 2


title: ATAC-seq for CD4-STAR-10nM Experiment-Replicate 2


title: ATAC-seq for CD4-STAR-100nM Experiment-Replicate 1


title: ATAC-seq for CD4-STAR-100nM Experiment-Replicate 2


title: ATAC-seq for CD4-TCR-noStimulation Experiment-Replicate 2


title: ATAC-seq for CD4-28zCAR-noStimulation Experiment-Replicate 2


title: ATAC-seq for CD4-STAR-100nM Experiment-Replicate 3


title: ATAC-seq for CD4-28zCAR-noStimulation Experiment-Replicate 3


title: ATAC-seq for CD4-28zCAR-noStimulation Experiment-Replicate 1


title: ATAC-seq for CD4-STAR-noStimulation Experiment-Replicate 1


title: ATAC-seq for CD4-28zCAR-10nM Experiment-Replicate 1


title: ATAC-seq for CD4-28zCAR-10nM Experiment-Replicate 3


title: ATAC-seq for CD4-28zCAR-1uM Experiment-Replicate 3


title: ATAC-seq for CD4-28zCAR-1uM Experiment-Replicate 2


title: ATAC-seq for CD4-28zCAR-100nM Experiment-Replicate 3


title: ATAC-seq for CD4-28zCAR-10nM Experiment-Replicate 2


title: ATAC-seq for CD4-28zCAR-1uM Experiment-Replicate 1


title: ATAC-seq for CD4-28zCAR-100nM Experiment-Replicate 1


title: SP4.GFP.HI.R3

city: San Francisco

first: Julie

last: Zikherman

address: 513 Parnassus Ave

department: Medicine, Rheumatology

institute: University of California, San Francisco

data_processing:
Raw sequencing reads were mapped to GRCm38 (mm10) with the GENCODE vM25 gene annotation using STAR v2.7.11b.
Differential gene expression analysis was performed using DESeq2 v1.34.0
Assembly: GRCm38 (mm10)
Supplementary files format and content: CSV file of gene-level TPMs and DESeq2 results

source_name: Thymus

extract_protocol:
Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research).
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: 10,000 cells were FACS sorted using the indicated markers into RLT + 1%BME and snap frozen.

value: Thymus

value: Semi-mature SP4

value: Nur77-eGFP BAC Tg

tag: phenotype

tag: sorting markers

value: Live CD25- CD69+ CD24+ CD4+ CD8- thymocytes


title: SP4.GFP.LOW.R2

tag: cell type


title: SP4.GFP.LOW.R3


title: SP4.GFP.MED.R3


title: ATAC-seq for CD4-28zCAR-100nM Experiment-Replicate 2

tag: treatment


title: SP4.GFP.HI.R2

tag: genotype


title: SP4.GFP.MED.R2


title: SP4.GFP.MED.R1


title: SP4.GFP.HI.R1


title: Live CD45+ Lin- liver cells 72hs post APAP

status: Public on Oct 30 2024

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent

description: GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq (version 4.0.0 and version 7.1.0)
Demultiplexed data was then processed using the Cell Ranger count pipeline (version 7.1.0).
Assembly: mm10
Supplementary files format and content: h5 file including raw gene count (output CellRanger)
Library strategy: CITEseq

extract_protocol: All Methods listed in De Ponti, Buijko et al. TREM2 expression delineates spatially restricted and ontogenically distinct hepatic macrophages populations required for tissue repair. Immunity. 2024.

value: liver

tag: strain

value: Live CD45+ Lin-

value: APAP 72h

tag: type

value: CITEseq

tag: platform

value: 10x Genomics – v3

tag: library

value: mRNA

tag: nraddedabs


title: Live CD45+ Lin- liver cells 72hs post APAP ADT

description: ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

value: ADT

tag: adt

value: CD44_TotalSeqA, Clec4f_TotalSeqA, RatIgG1l_TotalSeqA, Vsig4_TotalSeqA, CD11b_TotalSeqA, CD54_TotalSeqA, CD11a_TotalSeqA, CD38_TotalSeqA, Ly6G_TotalSeqA, CD62P_TotalSeqA, CD335_TotalSeqA, FolateReceptorB_TotalSeqA, CD206_TotalSeqA, CD366_TotalSeqA, CD29_TotalSeqA, CD86_TotalSeqA, mouseIgG1_v2_TotalSeqA, CD172a_TotalSeqA, CD127_TotalSeqA, Ly6A_E_Sca1_TotalSeqA, CD102_TotalSeqA, CD14_TotalSeqA, CD150_TotalSeqA, CD20_TotalSeqA, CD5_TotalSeqA, MHCII_IA_IE_TotalSeqA, Ly6C_TotalSeqA, CD11c_TotalSeqA, Mertk_TotalSeqA, CD304_TotalSeqA, CD357_TotalSeqA, CD43_TotalSeqA, CD278_TotalSeqA, CD73_TotalSeqA, CD8a_TotalSeqA, SiglecH_TotalSeqA, RatIgG1k_TotalSeqA, CD301a_TotalSeqA, CD301b_TotalSeqA, CD24_TotalSeqA, CD49f_TotalSeqA, CD63_TotalSeqA, CD62L_TotalSeqA, CD117_TotalSeqA, CD55_TotalSeqA, CD274_TotalSeqA, CD106_TotalSeqA, CD49d_TotalSeqA, CD27_TotalSeqA, CD134_TotalSeqA, Cx3cr1_TotalSeqA, F4_80_TotalSeqA, CD370_TotalSeqA, CD152_TotalSeqA, CD21_CD35_TotalSeqA, CD200_TotalSeqA, CD300LG_TotalSeqA, Tim4_TotalSeqA, CD4_TotalSeqA, CD62E_TotalSeqA, CD196_TotalSeqA, CD137_TotalSeqA, CD16_32_TotalSeqA, CD68_TotalSeqA, Esam_TotalSeqA, CD45R_B220_TotalSeqA, NK1.1_TotalSeqA, Xcr1_TotalSeqA, CD25_TotalSeqA, CD115_TotalSeqA, Erk1_TotalSeqA, CD19_TotalSeqA, CD69_TotalSeqA, CD169_Siglec1_TotalSeqA, CD15_TotalSeqA, CD207_TotalSeqA, CD192_TotalSeqA, CD8b_TotalSeqA, CD195_TotalSeqA, FceRIa_TotalSeqA, Klrg1_TotalSeqA, CD79b_TotalSeqA, mouseIgG2a_TotalSeqA, HamIgG_TotalSeqA, CD279_TotalSeqA, antiP2RY12_TotalSeqA, CD83_TotalSeqA, CD197_TotalSeqA, CD23_TotalSeqA, CD3e_TotalSeqA, CD183_TotalSeqA, mouseIgG2b_TotalSeqA, integrinB7_TotalSeqA, CD71_TotalSeqA, CD103_TotalSeqA, CD309_TotalSeqA.1, CD64_TotalSeqA, Madcam1_TotalSeqA, CD93_TotalSeqA, ratIgG2b_TotalSeqA, mouseIgG1_TotalSeqA, CD140a_TotalSeqA, PanendothelialCellAntigen_TotalSeqA, RatIgG2c_TotalSeqA, CD135_TotalSeqA, CD204_TotalSeqA, CD28_TotalSeqA, CD122_TotalSeqA, CD36_TotalSeqA, CD223_TotalSeqA, CD41_TotalSeqA, Notch1_TotalSeqA, CD326_TotalSeqA, antiKcc2_TotalSeqA, TCRg_TCRd_TotalSeqA, Ly6G_Ly6C_TotalSeqA, CD3_TotalSeqA, A0211_TotalSeqA, TCRb_TotalSeqA, CD309_TotalSeqA, IgD_TotalSeqA, antiIrf4_TotalSeqA, CD90_mouseCD90.1_TotalSeqA, TER119_ErythroidCells_TotalSeqA, CD163_TotalSeqA, CD45.1_TotalSeqA, TCR_Vb8.1_8.2_TotalSeqA, TCR_Vg1.1_Cr4_TotalSeqA, TCR_Vg3_TotalSeqA, CD45_TotalSeqA, antiGabrb3_TotalSeqA, antiRORg_TotalSeqA, CD90.2_TotalSeqA, RatIgG2a_TotalSeqA, CD49b_TotalSeqA, TCR_Vb5.1_5.2_TotalSeqA, CD201_TotalSeqA, CD45.2_TotalSeqA, TCR_Vg2_TotalSeqA, H2Kb_SIINFEKL_TotalSeqA, CD48_TotalSeqA, ReceptorD4_TotalSeqA, IgM_TotalSeqA, Ly6D_TotalSeqA

tag: adt added

value: Clec4f_TotalSeqA, Vsig4_TotalSeqA, RatIgG1l_TotalSeqA, CD44_TotalSeqA, CD11a_TotalSeqA, CD38_TotalSeqA, CD54_TotalSeqA, Ly6G_TotalSeqA, CD62P_TotalSeqA, CD278_TotalSeqA, CD14_TotalSeqA, Ly6A_E_Sca1_TotalSeqA, FolateReceptorB_TotalSeqA, CD86_TotalSeqA, CD206_TotalSeqA, CD335_TotalSeqA, MHCII_IA_IE_TotalSeqA, CD11b_TotalSeqA, CD366_TotalSeqA, CD150_TotalSeqA, mouseIgG1_v2_TotalSeqA, Ly6C_TotalSeqA, CD5_TotalSeqA, CD102_TotalSeqA, CD127_TotalSeqA, CD172a_TotalSeqA, CD301b_TotalSeqA, Mertk_TotalSeqA, CD43_TotalSeqA, CD55_TotalSeqA, Tim4_TotalSeqA, CD357_TotalSeqA, CD29_TotalSeqA, CD20_TotalSeqA, CD274_TotalSeqA, CD62L_TotalSeqA, RatIgG1k_TotalSeqA, CD63_TotalSeqA, CD73_TotalSeqA, CD117_TotalSeqA, CD8a_TotalSeqA, CD370_TotalSeqA, SiglecH_TotalSeqA, F4_80_TotalSeqA, CD27_TotalSeqA, CD301a_TotalSeqA, CD304_TotalSeqA, CD152_TotalSeqA, CD16_32_TotalSeqA, CD106_TotalSeqA, CD11c_TotalSeqA, CD4_TotalSeqA, CD300LG_TotalSeqA, CD21_CD35_TotalSeqA, CD309_TotalSeqA.1, CD134_TotalSeqA, CD200_TotalSeqA, CD49d_TotalSeqA, CD68_TotalSeqA, CD8b_TotalSeqA, CD169_Siglec1_TotalSeqA, CD62E_TotalSeqA, NK1.1_TotalSeqA, CD137_TotalSeqA, CD25_TotalSeqA, Erk1_TotalSeqA, CD196_TotalSeqA, Cx3cr1_TotalSeqA, Esam_TotalSeqA, CD19_TotalSeqA, CD192_TotalSeqA, CD79b_TotalSeqA, CD69_TotalSeqA, Xcr1_TotalSeqA, CD24_TotalSeqA, CD195_TotalSeqA, CD207_TotalSeqA, CD15_TotalSeqA, FceRIa_TotalSeqA, CD115_TotalSeqA, CD45R_B220_TotalSeqA, CD49f_TotalSeqA, Klrg1_TotalSeqA, CD197_TotalSeqA, CD83_TotalSeqA, CD23_TotalSeqA, CD183_TotalSeqA, HamIgG_TotalSeqA, integrinB7_TotalSeqA, CD103_TotalSeqA, CD279_TotalSeqA, antiP2RY12_TotalSeqA, CD93_TotalSeqA, mouseIgG2a_TotalSeqA, CD3e_TotalSeqA, mouseIgG2b_TotalSeqA, PanendothelialCellAntigen_TotalSeqA, Madcam1_TotalSeqA, CD140a_TotalSeqA, ratIgG2b_TotalSeqA, CD204_TotalSeqA, mouseIgG1_TotalSeqA, CD64_TotalSeqA, CD28_TotalSeqA, RatIgG2c_TotalSeqA, CD223_TotalSeqA, CD135_TotalSeqA, CD71_TotalSeqA, Notch1_TotalSeqA, CD41_TotalSeqA, CD122_TotalSeqA, CD36_TotalSeqA, CD326_TotalSeqA, antiKcc2_TotalSeqA


title: Live CD45+ Lin- Ly6C- liver cells 48hs post APAP ADT

value: Live CD45+ Lin- Ly6C-

value: APAP 48h


title: Live CD45+ Lin- Ly6C- liver cells post PBS

value: PBS


title: Live CD45+ Lin- Ly6C- liver cells 24hs post APAP ADT

value: APAP 24h


title: Live CD45+ Lin- Ly6C- liver cells 48hs post APAP


title: Live CD45+ Lin- Ly6C- liver cells 72hs post APAP


title: Live CD45+ Lin- Ly6C- liver cells 24hs post APAP


title: Live CD45+ Lin- Ly6C- liver cells post PBS ADT


title: Live CD45+ Lin- liver cells 48hs post APAP ADT


title: Live CD45+ Lin- liver cells post PBS


title: Live CD45+ Lin- liver cells 24hs post APAP


title: Liver Kcs 48hrs post APAP

value: Kcs

value: single cell RNA-seq


title: LAM-like liver Kcs 48hrs post APAP

value: LAM-like Kcs


title: Live CD45+ liver cells 72hrs post APAP

value: Live CD45+


title: Live CD45+ Lin- liver cells 24hs post APAP ADT

value: liver


title: Live CD45+ Lin- liver cells post PBS ADT

value: Live CD45+ Lin-


title: Live CD45+ Lin- liver cells 48hs post APAP


title: SP4.GFP.LOW.R1

value: Thymus

value: Semi-mature SP4

value: Nur77-eGFP BAC Tg

value: Live CD25- CD69+ CD24+ CD4+ CD8- thymocytes


title: Live CD45- liver cells 24hrs post APAP

value: Live CD45-

value: 10x Genomics – v3

value: mRNA


title: Live CD45+ liver cells 48hrs post APAP


title: Liver hepatocytes 24hrs post APAP

value: Hepatocytes


title: Live CD45- liver cells 72hrs post APAP

value: APAP 72h


title: Myeloid liver cells 48hrs post APAP, ADT

value: Myeloid

value: APAP 48h

value: CITEseq

value: 10x Genomics – v2

value: ADT

value: IgG1_Rat_l, CD11a, Ly6C, CD43, CD5, CD62L, CD150, CLEC4F, CD86, CD62P, CD300LG, CD25, CD278, VSIG4, CD11b_mh, CD304, CD38, CD301b, CD44_mh, CD49d, CD274, CD127, CD117, CD15_mh, Siglec, CD102, Panendothelial, CD14, ERK1, CX3CR1, Ly6G, CD63, CD62E, Folate, Tim4, IgG2a_Rat_k, Integrin, CD195, CD192, CD69, CD106, IA_IE, CD19, NK1_1, CD357, FceRIa, CD54, CD4, CD134, CD206, CD223, CD24, MERTK, CD335, CD152, IgG1_Rat_k, CD16_CD32, CD8a, CD11c, KLRG1_mh, CD140a, XCR1, IgG_Hamster, CD68, CD23, CD49f, MAdCAM1, CD79b, CD207_mh, CD55, CD103, CD73, CD137, CD20, Ly6A_Ly6E, CD83, CD169, CD279, CD301a, CD197, CD366, IgG2c_Rat_k, CD64, CD135, CD370, CD21_CD35, Notch, CD122, CD309_A0554, CD93, CD183, IgG2a_Mouse_k, CD27_A0191, CD28, F4_80, IgG1_Mouse_k, CD8b, CD45R_B220, CD204, ESAM, CD200, CD196, CD115, IgG2b_Rat_k, P2RY12, IgG2b_Mouse_k, CD3e, TCRgd, CD71, CD172a, CD163, CD90, Ly6G_Ly6C, CD45_A0178, CD309_A0553, CD3, CD326, CD45, TCRg, CD29, TER119, TCRb8, TCRb, IgD, IRF4, CD41, RORg, IgG2a, CXCR4, CD146, CD45_A0157, H2Kb, TCRg3, TCRb5, CD36, CD90_A0075, TCRg2, CD49b, CD48, ReceptorD4, GABRB3, biotin, KCC2, CD201, IgM, CD200R, CD193, CD200R3, CD138, CD317, CD105, CD9, P2X7R, CD371, CD22, CD39, CD314, DR3, IL33Ra, Ly49H, Ly49D, CD185, CD278.1, TIGIT, CD80, CD49a, CD1d, CD226, CD34, TLR4, CD300c_d, JAML, CD272, PIRA_PIRB, CD26, DLL1, CD270, 4_1BB, ENPP1, CD2, Mac2, CD31, CD107a, CD124, CD95, Streptavidin_A0951, Streptavidin_A0952, Streptavidin_A0953, Streptavidin_A0954, Streptavidin_A0955, Ly6D, CD170

value: IgG1_Rat_l, CD5, CD278, CD150, CD62P, CLEC4F, CD62L, CD86, VSIG4, CD11a, CD43, CD38, CD117, Ly6C, CD127, CD300LG, CD25, CD274, Tim4, MAdCAM1, CD195, CD304, CD301b, CD15_mh, Panendothelial, Siglec, ERK1, CD62E, CD63, IA_IE, CD102, CD192, CD106, CD357, CD69, Folate, CD19, CD14, NK1_1, CD4, CD335, Integrin, CD49d, CD134, CD223, FceRIa, MERTK, CD206, CD55, CD79b, CD44_mh, CD140a, Ly6G, CD8a, IgG1_Rat_k, Ly6A_Ly6E, IgG2a_Rat_k, CD370, CX3CR1, CD73, CD16_CD32, CD103, CD23, CD137, KLRG1_mh, CD68, CD207_mh, CD169, CD54, CD152, CD20, CD83, XCR1, CD21_CD35, CD11b_mh, CD197, IgG_Hamster, CD135, Notch, CD27_A0191, ESAM, CD183, CD366, IgG1_Mouse_k, CD122, CD45R_B220, IgG2c_Rat_k, CD309_A0554, CD93, CD8b, F4_80, CD11c, CD28, CD200, CD64, CD279, CD301a, CD24, CD204, CD49f, CD196, IgG2a_Mouse_k, IgG2b_Rat_k, CD115, IgG2b_Mouse_k, P2RY12, CD3e


title: Live CD45+ liver cells 24hrs post APAP

value: liver

value: Live CD45+

value: APAP 24h

value: single cell RNA-seq


title: Live CD45- liver cells 48hrs post APAP


title: Live CD45+ liver cells post PBS rep 2

value: PBS


title: Myeloid liver cells 48hrs post APAP, GEX


title: Myeloid liver cells 24hrs post APAP, ADT


title: Live CD45+ Lin- Ly6C- liver cells 72hs post APAP ADT

value: Live CD45+ Lin- Ly6C-

value: CD44_TotalSeqA, Clec4f_TotalSeqA, RatIgG1l_TotalSeqA, Vsig4_TotalSeqA, CD11b_TotalSeqA, CD54_TotalSeqA, CD11a_TotalSeqA, CD38_TotalSeqA, Ly6G_TotalSeqA, CD62P_TotalSeqA, CD335_TotalSeqA, FolateReceptorB_TotalSeqA, CD206_TotalSeqA, CD366_TotalSeqA, CD29_TotalSeqA, CD86_TotalSeqA, mouseIgG1_v2_TotalSeqA, CD172a_TotalSeqA, CD127_TotalSeqA, Ly6A_E_Sca1_TotalSeqA, CD102_TotalSeqA, CD14_TotalSeqA, CD150_TotalSeqA, CD20_TotalSeqA, CD5_TotalSeqA, MHCII_IA_IE_TotalSeqA, Ly6C_TotalSeqA, CD11c_TotalSeqA, Mertk_TotalSeqA, CD304_TotalSeqA, CD357_TotalSeqA, CD43_TotalSeqA, CD278_TotalSeqA, CD73_TotalSeqA, CD8a_TotalSeqA, SiglecH_TotalSeqA, RatIgG1k_TotalSeqA, CD301a_TotalSeqA, CD301b_TotalSeqA, CD24_TotalSeqA, CD49f_TotalSeqA, CD63_TotalSeqA, CD62L_TotalSeqA, CD117_TotalSeqA, CD55_TotalSeqA, CD274_TotalSeqA, CD106_TotalSeqA, CD49d_TotalSeqA, CD27_TotalSeqA, CD134_TotalSeqA, Cx3cr1_TotalSeqA, F4_80_TotalSeqA, CD370_TotalSeqA, CD152_TotalSeqA, CD21_CD35_TotalSeqA, CD200_TotalSeqA, CD300LG_TotalSeqA, Tim4_TotalSeqA, CD4_TotalSeqA, CD62E_TotalSeqA, CD196_TotalSeqA, CD137_TotalSeqA, CD16_32_TotalSeqA, CD68_TotalSeqA, Esam_TotalSeqA, CD45R_B220_TotalSeqA, NK1.1_TotalSeqA, Xcr1_TotalSeqA, CD25_TotalSeqA, CD115_TotalSeqA, Erk1_TotalSeqA, CD19_TotalSeqA, CD69_TotalSeqA, CD169_Siglec1_TotalSeqA, CD15_TotalSeqA, CD207_TotalSeqA, CD192_TotalSeqA, CD8b_TotalSeqA, CD195_TotalSeqA, FceRIa_TotalSeqA, Klrg1_TotalSeqA, CD79b_TotalSeqA, mouseIgG2a_TotalSeqA, HamIgG_TotalSeqA, CD279_TotalSeqA, antiP2RY12_TotalSeqA, CD83_TotalSeqA, CD197_TotalSeqA, CD23_TotalSeqA, CD3e_TotalSeqA, CD183_TotalSeqA, mouseIgG2b_TotalSeqA, integrinB7_TotalSeqA, CD71_TotalSeqA, CD103_TotalSeqA, CD309_TotalSeqA.1, CD64_TotalSeqA, Madcam1_TotalSeqA, CD93_TotalSeqA, ratIgG2b_TotalSeqA, mouseIgG1_TotalSeqA, CD140a_TotalSeqA, PanendothelialCellAntigen_TotalSeqA, RatIgG2c_TotalSeqA, CD135_TotalSeqA, CD204_TotalSeqA, CD28_TotalSeqA, CD122_TotalSeqA, CD36_TotalSeqA, CD223_TotalSeqA, CD41_TotalSeqA, Notch1_TotalSeqA, CD326_TotalSeqA, antiKcc2_TotalSeqA, TCRg_TCRd_TotalSeqA, Ly6G_Ly6C_TotalSeqA, CD3_TotalSeqA, A0211_TotalSeqA, TCRb_TotalSeqA, CD309_TotalSeqA, IgD_TotalSeqA, antiIrf4_TotalSeqA, CD90_mouseCD90.1_TotalSeqA, TER119_ErythroidCells_TotalSeqA, CD163_TotalSeqA, CD45.1_TotalSeqA, TCR_Vb8.1_8.2_TotalSeqA, TCR_Vg1.1_Cr4_TotalSeqA, TCR_Vg3_TotalSeqA, CD45_TotalSeqA, antiGabrb3_TotalSeqA, antiRORg_TotalSeqA, CD90.2_TotalSeqA, RatIgG2a_TotalSeqA, CD49b_TotalSeqA, TCR_Vb5.1_5.2_TotalSeqA, CD201_TotalSeqA, CD45.2_TotalSeqA, TCR_Vg2_TotalSeqA, H2Kb_SIINFEKL_TotalSeqA, CD48_TotalSeqA, ReceptorD4_TotalSeqA, IgM_TotalSeqA, Ly6D_TotalSeqA

value: Clec4f_TotalSeqA, Vsig4_TotalSeqA, RatIgG1l_TotalSeqA, CD44_TotalSeqA, CD11a_TotalSeqA, CD38_TotalSeqA, CD54_TotalSeqA, Ly6G_TotalSeqA, CD62P_TotalSeqA, CD278_TotalSeqA, CD14_TotalSeqA, Ly6A_E_Sca1_TotalSeqA, FolateReceptorB_TotalSeqA, CD86_TotalSeqA, CD206_TotalSeqA, CD335_TotalSeqA, MHCII_IA_IE_TotalSeqA, CD11b_TotalSeqA, CD366_TotalSeqA, CD150_TotalSeqA, mouseIgG1_v2_TotalSeqA, Ly6C_TotalSeqA, CD5_TotalSeqA, CD102_TotalSeqA, CD127_TotalSeqA, CD172a_TotalSeqA, CD301b_TotalSeqA, Mertk_TotalSeqA, CD43_TotalSeqA, CD55_TotalSeqA, Tim4_TotalSeqA, CD357_TotalSeqA, CD29_TotalSeqA, CD20_TotalSeqA, CD274_TotalSeqA, CD62L_TotalSeqA, RatIgG1k_TotalSeqA, CD63_TotalSeqA, CD73_TotalSeqA, CD117_TotalSeqA, CD8a_TotalSeqA, CD370_TotalSeqA, SiglecH_TotalSeqA, F4_80_TotalSeqA, CD27_TotalSeqA, CD301a_TotalSeqA, CD304_TotalSeqA, CD152_TotalSeqA, CD16_32_TotalSeqA, CD106_TotalSeqA, CD11c_TotalSeqA, CD4_TotalSeqA, CD300LG_TotalSeqA, CD21_CD35_TotalSeqA, CD309_TotalSeqA.1, CD134_TotalSeqA, CD200_TotalSeqA, CD49d_TotalSeqA, CD68_TotalSeqA, CD8b_TotalSeqA, CD169_Siglec1_TotalSeqA, CD62E_TotalSeqA, NK1.1_TotalSeqA, CD137_TotalSeqA, CD25_TotalSeqA, Erk1_TotalSeqA, CD196_TotalSeqA, Cx3cr1_TotalSeqA, Esam_TotalSeqA, CD19_TotalSeqA, CD192_TotalSeqA, CD79b_TotalSeqA, CD69_TotalSeqA, Xcr1_TotalSeqA, CD24_TotalSeqA, CD195_TotalSeqA, CD207_TotalSeqA, CD15_TotalSeqA, FceRIa_TotalSeqA, CD115_TotalSeqA, CD45R_B220_TotalSeqA, CD49f_TotalSeqA, Klrg1_TotalSeqA, CD197_TotalSeqA, CD83_TotalSeqA, CD23_TotalSeqA, CD183_TotalSeqA, HamIgG_TotalSeqA, integrinB7_TotalSeqA, CD103_TotalSeqA, CD279_TotalSeqA, antiP2RY12_TotalSeqA, CD93_TotalSeqA, mouseIgG2a_TotalSeqA, CD3e_TotalSeqA, mouseIgG2b_TotalSeqA, PanendothelialCellAntigen_TotalSeqA, Madcam1_TotalSeqA, CD140a_TotalSeqA, ratIgG2b_TotalSeqA, CD204_TotalSeqA, mouseIgG1_TotalSeqA, CD64_TotalSeqA, CD28_TotalSeqA, RatIgG2c_TotalSeqA, CD223_TotalSeqA, CD135_TotalSeqA, CD71_TotalSeqA, Notch1_TotalSeqA, CD41_TotalSeqA, CD122_TotalSeqA, CD36_TotalSeqA, CD326_TotalSeqA, antiKcc2_TotalSeqA


title: Myeloid liver cells post PBS, ADT


title: Myeloid liver cells post PBS, GEX

value: mRNA