title: macrophages, male, bcCML leukemia-associated macrophage, day 11, rep3

city: Rochester

first: Benjamin

middle: J

last: Frisch

state: NY

address: 601 Elmwood Ave

institute: University of Rochester School of Medicine and Dentistry

description: Library name: ML

data_processing:
Data Formatting - bcl2fastq 2.19.1
Data Cleaning - fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification - subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
DESeq2-1.28.1 within R-4.0.2 was used to perform data normalization and differential expression analysis
Assembly: GRCm39 + M31
Supplementary files format and content: raw gene counts for each sample with submission

source_name: macrophage

extract_protocol:
RNA was extracted from sorted cells using the Rneasy kit from Qiagen following manufacturers instructions.
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100. 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols.

value: macrophage

value: bcCML leukemia-associated macrophage


title: macrophages, female, bcCML leukemia-associated macrophage, day 11, rep3

status: Public on Mar 11 2026

type: SRA

country: USA

description: Library name: FL

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: treatment


title: HeLa siRNA KDEL Receptor 2, replica 4

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

description: Library name: siKR2_D4_R1.fastq.gz

data_processing:
Trimming of the adapter sequences from reads with Trimmomatic
Alignment to the human hg38 genome using the STAR (v2.5.3a)
Counting of genes using featureCounts with the gene annotation from Gencode (version31).
R/Bioconduction package ‘limma’ was used to conduct differential expression analysis using standard procedures.
Assembly: hg38
Supplementary files format and content: count_data.txt: raw counts of expressed genes (cpm>1 in at least 5 samples)
Supplementary files format and content: Palazzo_Differential_Expression_Limma.txt contains the results of the differential expression contrasts result of applying the limma::write.fit() function

molecule: polyA RNA

organism: Homo sapiens

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Euroclone) and Penicillin/Streptavidin (Pen/Strep).

extract_protocol:
72 hours after silencing cells were collected and RNA extracted using the RNeasy Plus Kits for RNA Isolation (QIAGEN, ID: 74134) and quantified by Nanodrop.
Libraries of cDNA were prepared with TruSeq mRNA Library Prep Kit (Illumina) and sequenced using the Novaseq instrument (Illumina) 100 bp single-end up to 30 million reads.

treatment_protocol: For silencing assays, cells were plated in 6 wells or 6 cm plates to have about 50-60% confluence on the day of transfection. Five replicates for each condition were used. Following the manufacturer's instruction, cells were transfected using Lipofectamine RNAiMAX (Invitrogen). MISSION® siRNA Universal Negative Control (MERCK) was used as a control. 3 µL duplexes (20 µM) were used for each well of a 6-well plate. Cells were incubated overnight at 37% and 5% CO2. The morning after, the supernatant was replaced with 2 mL of fresh medium. Cells were harvested and lysed 72 hours after silencing.

tag: tissue

value: uterine cervix

tag: cell line

value: Hela

value: siRNA with duplexes against KDELR2


title: macrophages, female, bcCML leukemia-associated macrophage, day 11, rep2

description: Library name: FR


title: macrophages, female, bcCML leukemia-associated macrophage, day 11, rep1

description: Library name: FN


title: LG-Null-rep1_ATAC

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

description: Library name: LG-Null-rep1_ATAC

library_source: genomic

data_processing:
ChIP-seq: Single-end reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome using the bwa2 mem. The duplicated reads were removed using the Picard Toolkit (https://broadinstitute.github.io/picard/), whereas the reads with a quality lower than 20 were filtered. The ChIP-seq peaks were called using the default (narrow) setting in MACS2.
ATAC-seq: The adapters were removed and the filtered reads were mapped to GRCm38/mm10 (or GRCh37/hg19) using bwa mem. The duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/) and the reads with quality lower than 20 were filtered.
RNA-seq: The reads were mapped toGRCm38/mm10 (or GRCh37/hg19) using STAR. The reads mapped to gene exon regions were counted using featureCounts. Differential expression was determined using DESeq2.
HiChIP: HiChIP data were processed using HiC-Pro with default parameters with the exception of the LIGATION_SITE being set to GATCGATC, GANTGATC, GANTANTC, GATCANTC and the GENOME_FRAGMENT that was generated using digest_genome.py in HiC-Pro utilities. The following parameters were used: -r ^GATC G ^ANTC -o mm10 (or hg19)_restriction sites.bed hg19.fasta. The raw reads were mapped to the GRCm38/mm10 (or GRCh37/hg19) reference genome and were assigned to restriction fragments. The raw reads were filtered for valid pairs (VI). 1D coverage files for the visualization in bigwig format were converted from bam format using deepTools and RPKM (Reads Per Kilobase per Million reads to normalize the number of reads per bin) normalization was used. The HiC files were generated using hicprotojuiebox.py utilities in HiC-Pro.
Assembly: GRCm38/mm10 (or GRCh37/hg19)

molecule: genomic DNA

source_name: umbilical vein

growth_protocol: Mouse aortic endothelial cells (isolated from mouse aorta) and human umbilical vein cells (Cell biology) were cultured in endothelial cell growth medium in T12.5 flasks coated with gelatin (0.1%). Incubate the cells at 37 °C, 5% CO2 until they are 85% - 90% confluent. After 2-3 passages, endothelial cells were treated with Trypsin-EDTA (0.25% Trypsin, 0.02 EDTA in PBS) and collected. The cells were washed with sterile 37 °C PBS before subsequent experiments.

extract_protocol:
ChIP-seq: Chromatin (8 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were precipitated using 4 μg of antibody against H3K27Ac (Active Motif, Cat# 39133) or 10 μg of antibody again JUNB (Activemotif, Cat#39549). The complexes were washed, eluted from the beads with 1% SDS buffer and subjected to RNase and proteinase K treatment overnight at 65°C. The ChIPed DNA was purified by phenol-chloroform extraction and ethanol precipitation. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K in a similar way as ChIPed DNA.
ATAC-seq: Cells grown in tissue culture were pretreated with 200 U/ml DNase (Worthington) for 30 min at 37 °C to remove free-floating DNA and to digest DNA from dead cells. This medium was then washed out, and the cells were resuspended in cold PBS. After the cells were counted, 50,000 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 g for 5 min at 4 °C. Supernatant was carefully aspirated. Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g at 4 °C. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2), 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down at least five times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator-5 kit.
RNA-seq: Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
H3K27ac HiChIP: Biotin-labeled proximally-ligated chromatin was prepared using the Arima-HiC kit (Arima Genomics Cat # A510008). Briefly, the crosslinked chromatin was initially digested using a restriction enzyme (RE) cocktail. The 5’-overhangs were subsequently filled in and labeled with a biotinylated nucleotide. Subsequently, the spatially proximal digested ends of DNA were ligated. The resulting proximally-ligated chromatin was fragmented using the Diagenode Bioruptor Pico instrument, bound to an H3K27ac antibody (Abcam Cat # ab4729) overnight and immunoprecipitated on Protein A magnetic beads (Thermo Cat # 10002D). The immunoprecipitated chromatin was reverse crosslinked and purified using the Arima-HiC kit. Subsequently, the Illumina-compatible sequencing libraries were prepared by initial enrichment for biotin using C1 streptavidin beads (Thermo Cat # 65001). The samples were tagmented on-bead utilizing Tagment DNA Enzyme and Buffer (Illumina Cat # 20034197). Subsequently, DNA was ready for PCR enrichment.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated. system (Apollo 342, Wafergen Biosystems/Takara). ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads. Adapter sequences were not trimmed during demultiplexing. ATAC-seq: Libraries were prepared as the description (Buenrostro et al., 2015). RNA-seq: After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA form the total RNA with kit. By using the fragmentation buffer, the mRNA and non-coding RNAs are fragmented into short fragments (about 200~700 bp), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand cDNA. The double strand cDNA is purified with QiaQuick PCR extraction kit and then used for end-polishing. Sequencing adapters are ligated to the fragments , then the second strand is degraded using UNG(Uracil-N-Glyosylase)finally. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification.The library products are ready for sequencing analysis via Illunima HiSeq 4000 or Hiseq X Ten. HiChIP: Tagmented DNA was PCR amplified utilizing NPM and the indexing primers from the Nextera XT DNA Library Prep kit (Illumina Cat # FC-131-1024). The PCR products were purified and size selected by 0.5X SPRI beads followed by 0.7X SPRI beads before sequencing.

value: umbilical vein

value: Endothelial cell of umbilical vein


title: Old tdTomato- mouse 3

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description:
Library name: 18-old-td-neg-5
Old tdTomato- mouse 3

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software. Aligned gene-level counts were processed in R using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: TSV of raw gene counts and CPM for all samples are included

source_name: Brain

extract_protocol:
Total RNA was then isolated using the RNeasy Micro Plus Kit (Qiagen) according to the manufacturer’s instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 TapeStation. Double standard complementary DNA (cDNA) was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, and cycles per burst 50 for 120 s. cDNA was blunt ended, had an A base added to the 3′ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 to 15 cycles using primers, incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Brain

value: Macrophages

tag: genotype

value: Ms4a3-cre, R26-tdTomato

tag: sample group

value: Old tdTomato- mouse


title: macrophages, female, non-leukemic, rep3

description: Library name: F3

value: non-leukemic macrophage


title: macrophages, male, bcCML leukemia-associated macrophage, day 11, rep2

description: Library name: MR


title: Old tdTomato+ mouse 3

description:
Library name: 16-old-td-pos-3
Old tdTomato+ mouse 3

value: Old tdTomato+ mouse


title: macrophages, male, bcCML leukemia-associated macrophage, day 11, rep1

description: Library name: MN


title: HeLa siRNA KDEL Receptor 2, replica 1

description: Library name: siKR2_A4_R1.fastq.gz


title: HeLa siRNA KDEL Receptor 2, replica 3

description: Library name: siKR2_C4_R1.fastq.gz


title: HAEC-927_ATAC

description: Library name: HAEC-927_ATAC

source_name: aorta

value: aorta

value: aortic endothelial cells


title: macrophages, female, non-leukemic, rep2

description: Library name: F2


title: HeLa siRNA KDEL Receptor 2, replica 2

description: Library name: siKR2_B4_R1.fastq.gz


title: HCAEC-559_ATAC

description: Library name: HCAEC-559_ATAC


title: Old tdTomato- mouse 2

description:
Library name: 17-old-td-neg-4
Old tdTomato- mouse 2


title: macrophages, female, non-leukemic, rep1

description: Library name: F1


title: Old tdTomato+ mouse 2

description:
Library name: 13-old-td-pos-2
Old tdTomato+ mouse 2


title: HAEC-486_ATAC

description: Library name: HAEC-486_ATAC


title: HAEC-739_ATAC

description: Library name: HAEC-739_ATAC


title: Old tdTomato- mouse

description:
Library name: 15-old-td-neg-3
Old tdTomato- mouse


title: HAEC-456_ATAC

description: Library name: HAEC-456_ATAC


title: macrophages, male, non-leukemic, rep3

description: Library name: M3


title: HeLa siRNA KDEL Receptor 1, replica 5

description: Library name: siKR1_E3_R1.fastq.gz

value: siRNA with duplexes against KDELR1


title: Old tdTomato+ mouse

description:
Library name: 12-old-td-pos-1
Old tdTomato+ mouse


title: HeLa siRNA KDEL Receptor 1, replica 3

description: Library name: siKR1_C3_R1.fastq.gz


title: HeLa siRNA KDEL Receptor 1, replica 4

description: Library name: siKR1_D3_R1.fastq.gz


title: macrophages, male, non-leukemic, rep1

description: Library name: M1


title: Young tdTomato+ mouse 2

description:
Library name: 10-young-td-pos-2
Young tdTomato+ mouse 2

value: Young tdTomato+ mouse


title: macrophages, male, non-leukemic, rep2

description: Library name: M2

value: macrophage


title: Young tdTomato+ mouse

description:
Library name: 8-young-td-pos-1
Young tdTomato+ mouse


title: HeLa siRNA ERp44, replica 5

description: Library name: siERp44_E2_R1.fastq.gz

value: siRNA with duplexes against ERp44


title: GFP+ BMT-treated mouse 2

description:
Library name: 7-GFP-pos-BMT
GFP+ BMT-treated mouse 2 (pooled from mice 8-10)

value: WT/UBC-GFP

value: GFP+ BMT-treated mouse


title: GFP- BMT-treated mouse 4

description:
Library name: 5-GFP-neg-BMT
GFP- BMT-treated mouse 4 (pooled from mice 8-10)

value: GFP- BMT-treated mouse


title: scRNA-seq of mouse microglia, MCAO Day 56, Zfp384 ASO

city: Yushima, Bunkyo-ku

first: Jun

last: Tsuyama

state: Tokyo

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

description:
Library name: scRNA_Mouse_Microglia_Day56_ASOZfp384
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from ASO-Zfp384-administered mouse brain on day 56 after stroke onset. ASOs were administered intracerebroventricularly on days 29 and 43 after stroke onset. Sequenced on DNBSEQ-G400.

data_processing:
Read mapping and counting were processed with the 10x Genomics Cell Ranger 6.0.1 with the mm10 reference genome assembly with the addition of dTomato RNA sequences and gene annotation provided by 10x Genomics.
The SC Transformation method incorporated in Seurat 4.3.0 was used for the normalization of spliced-read counts for the individual genes.
The single-cell gene expression profiles of the samples were integrated using the anchor-based integration method in Seurat. Ten groups with k-means were obtained by this integrated count matrix, which clustered the cells by the shared nearest neighbor approach implemented in Seurat.
The UMAP plots were generated with the Seurat Dimplot module by using the normalized spliced read counts.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Cell Ranger filtered_feature_bc_matrix output in MEX format (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).

source_name: brain

growth_protocol: All mice were maintained in a conventional facility at the Institute of Science Tokyo or Tokyo Metropolitan Institute of Medical Science in Tokyo, Japan. All experiments were approved by the Institutional Animal Research Committee of the Institute of Science Tokyo (approval number: A2025-011C2) and Tokyo Metropolitan Institute of Medical Science (approval number: 21-004). C57BL/6J mice were used for WT mice.

extract_protocol:
For microglia samples: Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). CD45(int)CD11b(int) cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific). For whole brain cell samples: Brain cells including neurons were isolated from adult ischemic brain according to the protocol established in the Allen Institute (Tasic et al., Nature 2018); the detailed experimental method was described previously (Nakamura et al., Neuron 2023).
Brain cells including neurons were isolated from adult ischemic brain according to the protocol established in the Allen Institute (Tasic et al., Nature 2018); the detailed experimental method was described previously (Nakamura et al., Neuron 2023). Single CD45(int)CD11b(int) cells or brain cells were loaded onto chromium chips with a capture target of 2,000 to 10,000 cells per sample. Libraries were prepared using Chromium Next GEM Single Cell 5′ Reagent Kits v2 (10x Genomics) for CD45(int)CD11b(int) cells or Chromium Next GEM Single-cell 3′ Reagent Kits v3.1 (10x Genomics) for brain cells, according to the manufacturer's protocol. On a DNBSEQ-G400 sequencer (MGI), obtained libraries were sequenced with a targeted sequencing depth of more than 50,000 read pairs per cell.

treatment_protocol: Transient brain ischemia, induced by middle cerebral artery occlusion (MCAO), was generated in male mice between 8 and 24 weeks of age, with a weight range of 20 to 30 g. Anesthesia was induced by 3% isoflurane with a mixture of 70% nitrous oxide and 30% oxygen, and maintained by 1% isoflurane during the operation. Silicone-coated monofilaments were inserted through the common carotid artery to occlude the origin of the middle cerebral artery. Reperfusion was facilitated by withdrawing the inserted monofilaments 60 minutes after MCAO. Head temperature was maintained at 36°C. Inclusion criteria required confirmation of a >60% reduction in cerebral blood flow using laser Doppler flowmetry. Sham-operated mice underwent the same surgical procedure without occlusion.

value: brain

value: microglia

value: wild-type

value: MCAO + ASO-Zfp384


title: GFP- BMT-treated mouse 3

description:
Library name: 4-GFP-neg-BMT
GFP- BMT-treated mouse 3 (pooled from mice 6-7)

value: Brain

value: Macrophages


title: HeLa siRNA KDEL Receptor 1, replica 2

description: Library name: siKR1_B3_R1.fastq.gz

value: uterine cervix

value: Hela


title: Young tdTomato- mouse

description:
Library name: 11-young-td-neg-2
Young tdTomato- mouse

value: Ms4a3-cre, R26-tdTomato

value: Young tdTomato- mouse


title: HeLa siRNA ERp44, replica 3

description: Library name: siERp44_C2_R1.fastq.gz


title: HeLa siRNA KDEL Receptor 1, replica 1

description: Library name: siKR1_A3_R1.fastq.gz

value: siRNA with duplexes against KDELR1


title: LG_Ctrl_JUNB

description: Library name: LG_Ctrl_JUNB

value: umbilical vein

value: Endothelial cell of umbilical vein

value: JUNB overexpressed

value: high glocose


title: HG_Ctrl_JUNB

description: Library name: HG_Ctrl_JUNB


title: GFP+ BMT-treated mouse

description:
Library name: 3-GFP-pos-BMT
GFP+ BMT-treated mouse (pooled from mice 1-5)

value: WT/UBC-GFP

value: GFP+ BMT-treated mouse


title: HG_RBBP6-KD_H3K27ac

description: Library name: HG_RBBP6-KD_H3K27ac


title: scRNA-seq of mouse brain cells, MCAO Day 28, Zfp384 ASO

description:
Library name: scRNA_Mouse_BrainCells_Day28_ASOZfp384
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single-cell 3′ v3.1) of total brain cells from ASO-Zfp384-administered mouse brain on day 28 after stroke onset. ASOs were administered intracerebroventricularly on days 8 and 22 after stroke onset. Sequenced on DNBSEQ-G400.

value: brain

value: brain cells


title: HeLa siRNA ERp44, replica 2

description: Library name: siERp44_B2_R1.fastq.gz

value: siRNA with duplexes against ERp44


title: HG_RBBP6-KD_JUNB

description: Library name: HG_RBBP6-KD_JUNB


title: scRNA-seq of mouse microglia, MCAO Day 56, ASO control

description:
Library name: scRNA_Mouse_Microglia_Day56_ASOcontrol
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from ASO-control-administered mouse brain on day 56 after stroke onset. ASOs were administered intracerebroventricularly on days 29 and 43 after stroke onset. Sequenced on DNBSEQ-G400.

value: microglia

value: wild-type

value: MCAO + ASO-control


title: HeLa siRNA ERp44, replica 4

description: Library name: siERp44_D2_R1.fastq.gz

value: uterine cervix


title: scRNA-seq of mouse brain cells, MCAO Day 14, wild-type

description:
Library name: scRNA_Mouse_BrainCells_Day14_WT
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single-cell 3′ v3.1) of total brain cells from mouse brain on day 14 after stroke onset. Sequenced on DNBSEQ-G400.

value: MCAO


title: LG_Ctrl_H3K27ac

description: Library name: LG_Ctrl_H3K27ac


title: HeLa siRNA ERp44, replica 1

description: Library name: siERp44_A2_R1.fastq.gz

value: Hela


title: LG-Null-2_H3K27ac

description: Library name: LG-Null-2_H3K27ac


title: HG_JUNB-OE_JUNB

description: Library name: HG_JUNB-OE_JUNB


title: scRNA-seq of mouse brain cells, sham surgery, wild-type

description:
Library name: scRNA_Mouse_BrainCells_Sham_WT
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single-cell 3′ v3.1) of total brain cells from sham-operated mouse brain. Sequenced on DNBSEQ-G400.

value: Sham surgery


title: HG_Null_JUNB

description: Library name: HG_Null_JUNB


title: scRNA-seq of mouse brain cells, MCAO Day 28, ASO control

description:
Library name: scRNA_Mouse_BrainCells_Day28_ASOcontrol
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single-cell 3′ v3.1) of total brain cells from ASO-control-administered mouse brain on day 28 after stroke onset. ASOs were administered intracerebroventricularly on days 8 and 22 after stroke onset. Sequenced on DNBSEQ-G400.


title: LG_Null_JUNB

description: Library name: LG_Null_JUNB

value: WT


title: HG_JUNB-OE_H3K27ac

description: Library name: HG_JUNB-OE_H3K27ac

value: umbilical vein


title: scRNA-seq of mouse microglia, MCAO Day 28, Zfp384 ASO

description:
Library name: scRNA_Mouse_Microglia_Day28_ASOZfp384
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from ASO-Zfp384-administered mouse brain on day 28 after stroke onset. ASOs were administered intracerebroventricularly on days 8 and 22 after stroke onset. Sequenced on DNBSEQ-G400.

value: MCAO + ASO-Zfp384


title: GFP- BMT-treated mouse 2

description:
Library name: 2-GFP-neg-BMT
GFP- BMT-treated mouse 2 (pooled from mice 4-5)

value: Brain

value: Macrophages

value: GFP- BMT-treated mouse


title: HeLa siRNA control, replica 5

description: Library name: CTRL_E1_R1.fastq.gz

value: siRNA control with scrambled duplexes


title: GFP- BMT-treated mouse

description:
Library name: 1-GFP-neg-BMT
GFP- BMT-treated mouse (pooled from mice 1-3)

value: WT/UBC-GFP


title: HeLa siRNA control, replica 4

description: Library name: CTRL_D1_R1.fastq.gz


title: B6129, Infected, 8wk, 3

city: Singapore

first: Amit

last: Singhal

address: 8A Biomedical Grove, Immunos #05-13

department: A*STAR Infectious Diseases Labs (ID Labs)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description: Library name: R13259

data_processing:
Raw sequencing reads in FASTQ format were aligned to the mouse reference genome GRCm39 using the STAR aligner (v2.7.10b). Gene-level counts were obtained with the featureCounts function from the Rsubread package (v2.8.2) in R. These counts were then transformed into log₂ RPKM values using the edgeR package (v4.4.2).
Assembly: GRCm39
Supplementary files format and content: Comma-separated values (CSV) file includes raw counts for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted from mouse CD8 T cells frozen in TRIzol (Thermo Fisher), using acid guanidinium thiocyanate-phenol-chloroform extraction followed by a Qiagen RNeasy Micro clean-up procedure.
RNA was analyzed on Agilent Bioanalyser for quality assessment. cDNA libraries were prepared using 2 ng of total RNA using the Smart-seq2 protocol (Picelli et al, PMID: 24385147) with the following modifications: 1. Addition of 20 µM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip.

value: Spleen

value: CD8 T cells

value: Mtb-infected, 8wk


title: LG_Null_H3K27ac

description: Library name: LG_Null_H3K27ac

value: Endothelial cell of umbilical vein

value: low glucose


title: scRNA-seq of mouse microglia, MCAO Day 28, Zfp384 cKO

description:
Library name: scRNA_Mouse_Microglia_Day28_Zfp384cKO
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from Cx3cr1-CreER;Zfp384flox/flox mouse brain on day 28 after stroke onset. Sequenced on DNBSEQ-G400.

value: brain

value: microglia

value: Zfp384 cKO (DBD deletion) (Cx3cr1-CreER; Zfp384 flox/flox)


title: B6129, Infected, 8wk, 2

description: Library name: R13258


title: B6129, Infected, 8wk, 1

description: Library name: R13257


title: HeLa siRNA control, replica 1

description: Library name: CTRL_A1_R1.fastq.gz

value: uterine cervix

value: Hela


title: scRNA-seq of mouse microglia, MCAO Day 14, Igf1-CreER;Ai14

description:
Library name: scRNA_Mouse_Microglia_Day14_Igf1-CreER_Ai14
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from Igf1-CreER;Ai14 mouse brain on day 14 after stroke onset. Sequenced on DNBSEQ-G400.

value: Igf1-CreER; Ai14

value: MCAO


title: Co-housed_KO__Rep4_aorta

city: Los Angeles

first: Ekaterina

last: Koltsova

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description:
Library name: AOF23118
Raw counts_aorta.csv

data_processing:
RSEM along with bowtie2 used for alignment
Assembly: Mouse mm10
Supplementary files format and content: csv files inclued raw counts for each sample

extract_protocol:
RNA was harvested using Aurum™ Total RNA Fatty and Fibrous Tissue Kit
Illumina‑compatible mRNA library preparation (polyA enrichment or stranded mRNA‑seq) performed by Novogene

value: aorta

value: Co-housed


title: scRNA-seq of mouse microglia, MCAO Day 28, ASO control

description:
Library name: scRNA_Mouse_Microglia_Day28_ASOcontrol
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from ASO-control-administered mouse brain on day 28 after stroke onset. ASOs were administered intracerebroventricularly on days 8 and 22 after stroke onset. Sequenced on DNBSEQ-G400.

value: wild-type

value: MCAO + ASO-control


title: HG_Null_H3K27ac

description: Library name: HG_Null_H3K27ac

value: umbilical vein

value: WT


title: scRNA-seq of mouse microglia, sham surgery, wild-type

description:
Library name: scRNA_Mouse_Microglia_Sham_WT
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from sham-operated mouse brain. Sequenced on DNBSEQ-G400.

value: Sham surgery


title: Nr4a1-KO, Infected, 8wk, 3

description: Library name: R13256

value: Spleen

value: CD8 T cells

value: Mtb-infected, 8wk


title: HeLa siRNA control, replica 3

description: Library name: CTRL_C1_R1.fastq.gz

value: siRNA control with scrambled duplexes


title: bone marrow, P2rX7C

city: Beijing

first: Zimeng

last: Zhuang

address: Haidian District

department: Department of Orthodontics

country: China

institute: Peking University School and Hospital of Stomatology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: The processed data file (FPKM_all.txt) contained raw counts and FPKM values for each sample.

source_name: bone marrow

extract_protocol:
6-8 weeks WT or P2rx7 knockout mouse femurs were collected the bone marrow were flushed out. RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: P2rx7 knockout


title: Co-housed_KO__Rep5_aorta

description:
Library name: AOF23119
Raw counts_aorta.csv


title: Co-housed_KO__Rep3_aorta

description:
Library name: AOF23117
Raw counts_aorta.csv


title: Nr4a1-KO, Infected, 8wk, 1

description: Library name: R13254


title: HeLa siRNA control, replica 2

description: Library name: CTRL_B1_R1.fastq.gz

value: uterine cervix


title: Co-housed_KO__Rep2_aorta

description:
Library name: AOM23116
Raw counts_aorta.csv


title: PMN_isotype_2

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

description: Library name: Sample_11

data_processing:
Sequence reads were processed using Qiagen's software CLC Genomics workbench (v22.0.1) with CLC's default settings for RNA-Seq analysis (Reference sequence = Homo sapiens (GRCh38); Gene track = Homo sapiens (GRCh38.104); mRNA track = Homo sapiens (GRCh38.104); Use spike-in controls = no; Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0,8; Similarity fraction = 0,8; Global alignment = No; Strand specific = Both; Library type = Bulk; Maximum number of hits for a read = 10; Count paired reads as two = No; Ignore broken pairs = Yes; Expression value = TPM). Reads were aligned to GRCh38 genome. Expression value unit is TPM.
Assembly: GRCh38; GRCh38.104
Supplementary files format and content: tab-delimited text files; include feature Ids, total gene reads as well as TPM and RPKM for each sample.

source_name: peripheral blood

growth_protocol: PMN were isolated from fresh heparinized venous blood of healthy volunteers by density gradient sedimentation using a dextran solution followed by density gradient centrifugation using Histopaque 1077 (Sigma-Aldrich, St. Louis, MO, USA). The pelleted cells were treated with ammonium-chloride-potassium buffer for lysis of residual erythrocytes and resuspended in medium followed by checking for purity (CD11b and CD66b coexpression, average > 95%) by flow cytometry.

extract_protocol:
After activation, PMN were stained with PB-labeled anti-CD11b, FITC-labeled anti-CD66b, and APC-labeled anti-human CD62L (clone DREG-56, BioLegend). Activation and degranulation were determined as upregulation of CD11b or CD66b or as downregulation of CD62L. PMN activation or degranulation after stimulation with LPS or anti-TREM-1 (1C5) served as inclusion criteria, and PMN activation in the medium control group (preactivation) or after treatment with the isotype (4C9) were defined as exclusion criteria (33).
Barcoded mRNA seq libraries were prepared from 200 ng total RNA. For library preparation at Novogene, the mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNAenrichment. Subsequently, mRNA was randomly fragmented and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain is finished, the second chain is synthesized with the addition of an Illumina buffer. With this and together with the presence of dNTPs, RNase H and polymerase I from E.coli, the second chain is obtained by Nick translation. The resulting products go through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries have been pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount. Sequencing strategy was paired-end 150 cycles (PE150).

treatment_protocol: After each purification, PMN were investigated for activation and degranulation by flow cytometry to exclude preactivated PMN. Therefore, PMN were treated with LPS (lipopolysaccharides from Salmonella enterica serotype Typhimurium (Sigma-Aldrich) at a final concentration of 1µg/mL) or anti-TREM-1 compared to isotype control as well as unstimulated PMN for 30 min at 37°C. For TREM-1 ligation, 48-well or 96-well plates were coated with a mouse monoclonal anti-human TREM-1 antibody (clone 1C5) or mouse IgG1 (clone 4C9) serving as isotype matched control, both purified from hybridoma supernatants and used at 10 µg/mL PBS (32).

value: peripheral blood

value: purified neutrophils (PMN)


title: PMN_isotype_3

description: Library name: Sample_12


title: bone marrow, P2rX7B


title: Co-housed_KO__Rep1_aorta

description:
Library name: AOM23115
Raw counts_aorta.csv


title: PMN_isotype_1

description: Library name: Sample_10


title: B6129, Infected, 4wk, 3

description: Library name: R13253

value: Mtb-infected, 4wk


title: bone marrow, P2rX7A


title: PMN_TREM-1_3

description: Library name: Sample_9


title: Nr4a1-KO, Infected, 8wk, 2

description: Library name: R13255


title: scRNA-seq of mouse microglia, MCAO Day 28, Zfp384 flox/flox control

description:
Library name: scRNA_Mouse_Microglia_Day28_Zfp384flox
Single-cell RNA-seq (10x Genomics Chromium Next GEM Single Cell 5′ v2) of FACS-sorted CD45(int)CD11b(int) microglia from Zfp384flox/flox mouse brain on day 28 after stroke onset. Sequenced on DNBSEQ-G400.

value: brain

value: microglia

value: MCAO


title: PMN_TREM-1_2

description: Library name: Sample_8


title: bone marrow, WT3


title: Co-housed_WT__Rep3_aorta

description:
Library name: AOF23113
Raw counts_aorta.csv

value: aorta

value: Co-housed


title: B6129, Infected, 4wk, 2

description: Library name: R13252

value: WT


title: Co-housed_WT__Rep4_aorta

description:
Library name: AOF23114
Raw counts_aorta.csv


title: bone marrow, WT2


title: PMN_TREM-1_1

description: Library name: Sample_7


title: Co-housed_WT__Rep2_aorta

description:
Library name: AOM23112
Raw counts_aorta.csv


title: Nr4a1-KO, Infected, 4wk, 3

description: Library name: R13250


title: PMN_TLR4_3

description: Library name: Sample_6

value: LPS


title: bone marrow, WT1


title: Co-housed_WT__Rep1_aorta

description:
Library name: AOM23111
Raw counts_aorta.csv


title: Nr4a1-KO, Infected, 4wk, 1

description: Library name: R13248

value: Spleen


title: Abx_KO_Rep4_aorta

description:
Library name: AOM23_104
Raw counts_aorta.csv

value: Abx


title: PMN_medium_3

description: Library name: Sample_3

value: Medium


title: Eµ-MYC spleen lymphoma scRNA-seq M2_L002

city: Charlottesville

first: Jing

last: Gao

state: VA

address: 21 HOSPITAL DR, OMS BLOG RM 4767

department: Pathology

institute: University of Virginia

description:
Library name: EuMYC_M2_spleen_scRNA_L002
Eμ-Myc lymphoma spleen treated with S63845

data_processing:
Raw base call files were demultiplexed and converted to FASTQ format using Illumina bcl2fastq.
Reads were aligned to the reference genome and gene-level UMI counts were generated using Cell Ranger software (10x Genomics).
Downstream quality control, normalization, and exploratory analyses were performed using standard single-cell RNA-seq analysis workflows.
Assembly: Human: GRCh38; Mouse: GRCm38
Supplementary files format and content: Processed single-cell RNA-seq gene expression data were generated using Cell Ranger and provided in 10x Genomics format. For each sample, the processed data include a sparse gene-cell count matrix (matrix.mtx.gz), corresponding cell barcode annotations (barcodes.tsv.gz), and gene feature annotations (features.tsv.gz).

growth_protocol: Human Namalwa lymphoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and antibiotics at 37°C with 5% CO₂. Eu-Myc mouse lymphoma cells were isolated from spleen tissue and processed immediately for downstream single-cell RNA sequencing.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Single Cell 3′ platform according to the manufacturer’s instructions.

treatment_protocol: Namalwa cells were treated with the MCL-1 inhibitor S63845 or vehicle control for the indicated durations (12 h, 72 h， 8weeks) or subjected to long-term drug exposure to generate drug-resistant populations. Mouse lymphoma-bearing animals were treated as described in the associated study design.


title: PMN_TLR4_2

description: Library name: Sample_5


title: Abx_KO_Rep5_aorta

description:
Library name: AOM23_105
Raw counts_aorta.csv


title: PMN_TLR4_1

description: Library name: Sample_4


title: Eµ-MYC spleen lymphoma scRNA-seq M2_L001

description:
Library name: EuMYC_M2_spleen_scRNA_L001
Eμ-Myc lymphoma spleen treated with S63845


title: Nr4a1-KO, Infected, 2wk, 2

description: Library name: R13246

value: CD8 T cells

value: Mtb-infected, 2wk


title: PMN_medium_2

description: Library name: Sample_2


title: Abx_KO_Rep3_aorta

description:
Library name: AOM23_103
Raw counts_aorta.csv


title: Nr4a1-KO, Infected, 2wk, 3

description: Library name: R13247


title: B6129, Infected, 4wk, 1

description: Library name: R13251


title: Nr4a1-KO, Infected, 2wk, 1

description: Library name: R13245


title: Eµ-MYC spleen lymphoma scRNA-seq M1_L001

description:
Library name: EuMYC_M1_spleen_scRNA_L001
Eμ-Myc lymphoma spleen treated with S63845


title: Abx_KO_Rep2_aorta

description:
Library name: AOM23_102
Raw counts_aorta.csv


title: PMN_medium_1

description: Library name: Sample_1


title: Eµ-MYC spleen lymphoma scRNA-seq V2_L002

description:
Library name: EuMYC_V2_spleen_scRNA_L002
Eμ-Myc lymphoma spleen, vehicle control

value: Vehicle


title: Nr4a1-KO, Infected, 4wk, 2

description: Library name: R13249


title: Abx_KO_Rep1_aorta

description:
Library name: AOM23_101
Raw counts_aorta.csv


title: B6129, Infected, 2wk, 2

description: Library name: R13243


title: Eµ-MYC spleen lymphoma scRNA-seq V2_L001

description:
Library name: EuMYC_V2_spleen_scRNA_L001
Eμ-Myc lymphoma spleen, vehicle control


title: Eµ-MYC spleen lymphoma scRNA-seq M1_L002

description:
Library name: EuMYC_M1_spleen_scRNA_L002
Eμ-Myc lymphoma spleen treated with S63845


title: B6129, Infected, 2wk, 3

description: Library name: R13244


title: H2228 cells, crizotinib-resistant 2-biol rep3

city: Yongin-si

first: Dawon

last: Hong

state: Gyeonggi-do

address: 152 Jukjeon-ro

country: South Korea

institute: Dankook University

description: Library name: Sample 9

data_processing:
Genomic Data Commons (GDC)-based RNA-seq analysis pipeline
Adapter trimming and length filtering were performed using Cutadapt v3.4, ensuring high-quality reads. Trimmed reads were aligned to the human reference genome (GRCh38.p13, Ensembl release 100) using STAR v2.7.3a with a two-pass alignment strategy to improve splice junction detection. Read counts were quantified using HTSeq v0.12.4 in union mode.
Assembly: GRChg38(p13_ENS100)
Supplementary files format and content: comma separated values (csv) file, gene expression matrix in TPM

source_name: Lung

growth_protocol: H2228 lung adenocarcinoma cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using a Quick-RNA MiniPrep Plus kit (Zymo). 1.0 ug of total RNA was used to construct sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep kit following the manufacturer’s protocols.

value: Lung

value: lung adenocarcinoma

value: crizotinib for 8 months


title: H2228 cells, crizotinib-resistant 2-biol rep2

description: Library name: Sample 8


title: Eµ-MYC spleen lymphoma scRNA-seq V1_L002

description:
Library name: EuMYC_V1_spleen_scRNA_L002
Eμ-Myc lymphoma spleen, vehicle control


title: B6129, Infected, 2wk, 1

description: Library name: R13242


title: Nr4a1-KO, Uninfected, 3

description: Library name: R13241

value: Uninfected


title: Abx_WT_Rep3_aorta

description:
Library name: AOM23_108
Raw counts_aorta.csv


title: Eµ-MYC spleen lymphoma scRNA-seq V1_L001

description:
Library name: EuMYC_V1_spleen_scRNA_L001
Eμ-Myc lymphoma spleen, vehicle control


title: Abx_WT_Rep4_aorta

description:
Library name: AOM23_109
Raw counts_aorta.csv


title: H2228 cells, crizotinib-resistant 1-biol rep3

description: Library name: Sample 6


title: Nr4a1-KO, Uninfected, 2

description: Library name: R13240


title: mutant GPLD1 OE 1

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

address: 513 Parnassus Ave, Med. Sci. Bldg, Room S1364

institute: UCSF

description: snRNA seq

library_source: transcriptomic single cell

data_processing:
fastq files were generated using bcl2fastq by CellRanger by 10x Genomics
fastq files were converted to filtered count matrices using CellRanger count by 10xGenomics
Assembly: mm10
Supplementary files format and content: HDF5 matrix files

source_name: hippocampus

extract_protocol: nuclei were isolated, FACS sorted, and cDNA was synthesized using 3' scRNA seq protocols by 10x Genomics

value: hippocampus

value: nuclei


title: Nr4a1-KO, Uninfected, 1

description: Library name: R13239


title: Abx_WT_Rep2_aorta

description:
Library name: AOM23_107
Raw counts_aorta.csv


title: Separately_housed_KO_Rep6_aorta

description:
Library name: AOM110
Raw counts_aorta.csv


title: H2228 cells, crizotinib-resistant 1-biol rep2

description: Library name: Sample 5


title: GPLD1 OE 1

description: snRNA seq


title: Abx_WT_Rep1_aorta

description:
Library name: AOM23_106
Raw counts_aorta.csv


title: H2228-biol rep3

description: Library name: Sample 3


title: Abx_WT_Rep5_aorta

description:
Library name: AOM23_110
Raw counts_aorta.csv


title: H2228 cells, crizotinib-resistant 1-biol rep1

description: Library name: Sample 4


title: H2228 cells, crizotinib-resistant 2-biol rep1

description: Library name: Sample 7


title: B6129, Uninfected, 2

description: Library name: R13237


title: Alpl inhibitor 2

description: snRNA seq


title: Separately_housed_KO_Rep5_aorta

description:
Library name: AOM109
Raw counts_aorta.csv


title: H2228-biol rep2

description: Library name: Sample 2


title: GPLD1 OE 2

description: snRNA seq


title: Alpl inhibitor 1

description: snRNA seq


title: B6129, Uninfected, 1

description: Library name: R13236


title: H2228-biol rep1

description: Library name: Sample 1


title: Separately_housed_KO_Rep4_aorta

description:
Library name: AOM108
Raw counts_aorta.csv


title: Tumor-CD36-LepR-double positive-5

city: Brookline

first: Guangqing

last: Lu

state: MA

address: 1131 Beacon street, apt 4

institute: HMS

description:
Library name: Sample38
CD36-LepR-double positive replicate 5
LIB062306_TRA00279108_T-DP5-36_LEPR_S12

data_processing:
Raw sequencing reads were aligned to the Ensembl genome reference GRCm38, and gene counts were quantified using Salmon (v.1.8.0).
Assembly: GRCm38
Supplementary files format and content: csv files

source_name: Tumor

extract_protocol:
IECs were isolated from the ileum of SFB colonized mice, and immune cells were isolated from the spleens, mLNs, and tumors and stained as described above. Fresh cells were sorted directly into RLT buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), according to the manufacturer’s protocol.
The quality and quantity of the extracted RNAs were assessed using Bioanalyzer RNA Pico (Agilent). mRNA pull-down and cDNA synthesis were performed using the SMART-seq v4 kit (Takara), followed by library preparation using the Nextera XT DNA Library Prep Kit (Illumina).

value: Tumor

value: WT mice

value: CD36-LepR-double positive CD8 T cells

tag: batch


title: B6129, Uninfected, 3

description: Library name: R13238

value: WT


title: Single-nucleus sequencing of rice at the booting stage of the node

city: KunMing

first: Hu

last: Li

state: Yunnan

address: Yunnan University

institute: agricultural college

description: Library name: RNA3

data_processing:
snRNA-seq data processing was performed using Cell Ranger v6.1.2 (10× Genomics). Raw Illumina NovaSeq 6000 sequencing data (paired-end 150 bp reads) were first demultiplexed into fastq files using cellranger mkfastq. Subsequently, cellranger count was used to align reads to the Oryza sativa Japonica Group reference genome (IRGSP-1.0), quantify Unique Molecular Identifiers (UMIs), and generate gene-nucleus count matrices. Low-quality nuclei (with <200 detected genes or >20% mitochondrial reads) and low-expression genes (detected in <3 nuclei) were filtered out to obtain the final processed expression matrix.
Assembly: Oryza sativa Japonica Group (cv. Nipponbare) T2T genome assembly (GenBank Assembly ID: GCF_009914755.1, also known as Os-Nipponbare-T2T).
Supplementary files format and content: Processed data files follow standard 10× Genomics CellRanger format (aligned to Oryza sativa Nipponbare T2T genome), including gzipped barcodes.tsv.gz (quality-controlled nuclear barcodes), features.tsv.gz (T2T-based gene annotations), and matrix.mtx.gz (raw UMI counts in sparse MTX format); together they form a complete expression matrix compatible with tools like Seurat and Scanpy.

molecule: nuclear RNA

organism: Oryza sativa Japonica Group

source_name: node I

growth_protocol: Oryza sativa Japonica Group (cv. Nipponbare) were hydroponically grown in 1/2 Kimura B nutrient solution (pH 5.5–5.8, replaced every 2 days) under a humidified atmosphere with 12 h light (30000 lux, 30°C)/12 h dark (26°C) and 60%–70% relative humidity, until filling stage、flowering stage、booting stage.

extract_protocol:
Nuclei were extracted from node I tissues of Oryza sativa. Fresh node I samples were processed to isolate nuclei, which were then resuspended in PBS containing 0.04% BSA. Isolated nuclei from each developmental stage were prepared as input for library construction, following the nuclei isolation procedures compatible with the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10× Genomics) workflow.
snRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10× Genomics) on a Chromium Controller. Isolated nuclei from node I (resuspended in PBS with 0.04% BSA) were loaded separately by developmental stage onto Chromium Next GEM Chip G to generate single-cell gel beads in emulsion (GEMs) following the manufacturer’s instructions. Captured nuclei were lysed, and released RNA was reverse-transcribed to produce barcoded, full-length cDNA. Libraries were constructed per the kit protocol, with quality assessed using Qubit 4.0 Fluorometer and Agilent 2100 Bioanalyzer.

treatment_protocol: Oryza sativa Japonica Group (cv. Nipponbare) received no experimental treatment; plants were maintained under routine hydroponic conditions (1/2 Kimura B nutrient solution, pH 5.6–5.8, replaced every 2 days) until filling stage、flowering stage、booting stage.

tag: Stage

value: at the booting stage of the node

value: node I

tag: sample type

value: mixed population from panicle axis node I

value: None (no experimental treatment)


title: P8, replicate 1, scRNAseq

city: NEW YORK

first: Ya-Wen

last: Chen

address: 1425 MADISON AVE, Icahn 13-20A, Box 1189

department: Otolaryngology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Preprocessing of raw data was performed using CellRanger v7. Data were next normalized, scaled using Seurat v4. Low quality cells were filtered-out using miQC and data were integrated using Harmony. To identify cell types, we used the reference dataset of human lung GSE135893 and GSE136831 to guide cell type annotation with the package SingleR. Visualization of gene expression was performed with the VlnPlot function in Seurat or the package Nebulosa.
Assembly: hg38
Supplementary files format and content: Tab-separated values files adn matrix files

source_name: lung

extract_protocol:
Human lung tissue was washed with cold 1X PBS twice in a 10 cm petri dish and placed in digestion media containing dispase (5 U/ml, Corning 354535), Collagnease type I (478 U/ml, Thermo Scientific 17100017), DNase I (10 U/ml, Sigma-Aldrich 10104159001) in DMEM-F12 (Corning MT 10-092-CV). Tissues were digested for 1 hour at 37°C. After digestion, the cell suspension was filtered through 100-µm strainer (Corning 352360). Red blood cells were removed using Red Blood Cell Lysis Buffer. Cells were washed twice with FACS buffer (1% FBS, 1mM EDTA in PBS) and filtered through a 40-μm strainer (Corning 352340), pelleted again (450xg, 5 min, 4 °C), and resuspended in PBS containing Zombie Aqua™ Fixable Viability Kit (BioLegend 423101) for 20 minutes. Cells were washed and resuspend in FACS buffer with Human TruStain FcX (BioLegend 422302) for 10 minutes to block non-specific binding of antibodies
RNA-seq libraries were prepared based on the 10X Genomics protocol (CG000315 Rev E) using 10000 nuclei per replicate. Single-cell separation was performed using the Chromium Next GEM Chip G Single Cell Kit. The RNA-seq libraries were sequenced in paired-end mode on an Illumina Novaseq platform with the Novaseq S4 flowcell.

value: lung


title: Separately_housed_KO_Rep3_aorta

description:
Library name: AOM107
Raw counts_aorta.csv

value: aorta


title: Tumor-CD36-LepR-double positive-3

description:
Library name: Sample36
CD36-LepR-double positive replicate 3
LIB062306_TRA00279106_T-DP3-36_LEPR_S10


title: Separately_housed_KO_Rep2_aorta

description:
Library name: AOF102
Raw counts_aorta.csv


title: P7, replicate 1, scRNAseq


title: Tumor-CD36-LepR-double positive-4

description:
Library name: Sample37
CD36-LepR-double positive replicate 4
LIB062306_TRA00279107_T-DP4-36_LEPR_S11


title: Separately_housed_KO_Rep1_aorta

description:
Library name: AOF101
Raw counts_aorta.csv


title: P6, replicate 1, scRNAseq


title: Single-nucleus sequencing of rice at the filling stage of the node

description: Library name: RNA1

value: at the filling stage of the node


title: Tumor-CD36-LepR-double positive-1

description:
Library name: Sample34
CD36-LepR-double positive replicate 1
LIB062306_TRA00279104_T-DP1-36_LEPR_S8


title: Separately_housed_WT_Rep5_aorta

description:
Library name: AOM112
Raw counts_aorta.csv


title: Separately_housed_WT_Rep4_aorta

description:
Library name: AOM111
Raw counts_aorta.csv


title: SB_12wk_3x_3

city: Fargo

first: Evandro

last: Fortini

address: 1605 Albrecht Blvd N

institute: United States Department of Agriculture

description: Library name: PPP3_63

data_processing:
Paired-end reads obtained from the Novaseq 6000 system were processed using Trimmomatic to trim low-quality bases and remove adapter sequences, applying the parameters HEADCROP:10, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the Solanum tuberosum genome assembly version 6.1 (DM1-3516 R44) using HISAT2 (--dta). The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools. Transcript abundance was quantified with StringTie (-e, -B flags) using the reference genome annotation in GFF3 format. Gene and transcript count matrices were generated with the prepDE.py3 script.
Assembly: The Solanum tuberosum genome assembly version 6.1 was used for read alignment and analysis. The genome assembly, annotation, and related resources are available in the SpudDB database (Pham et al., 2020; https://spuddb.uga.edu/).
Supplementary files format and content: The processed data files include tab-delimited text files containing gene and transcript count matrices (gene_count_matrix.txt and transcript_count_matrix.txt). These files provide quantified expression levels for differential expression analysis, generated using the prepDE.py3 script based on StringTie outputs.

organism: Solanum tuberosum

source_name: Secondary Meristem

extract_protocol:
To extract RNA from primary and secondary meristem samples, roughly 100 mg of tissue was utilized following the protocol described by Rubio-Piña and Zapata-Pérez (2011). Similarly, for flesh tuber RNA extraction, approximately 200 mg of tissue was processed according to the procedure reported by Vennapusa et al. (2020). RNA quality, purity (OD260/280 and OD260/230), and concentration were confirmed using 1% agarose gel electrophoresis, Nanodrop One and Agilent 5400 Bioanalyzer.
RNA-seq

value: Secondary Meristem

value: Russet Burbank (Solanum tuberosum L.)


title: DMSO_POSTIMP

city: barcelona

first: aintzane

last: rueda

state: Choose State

address: C/ del Dr. Trueta, 179, 08005 Barcelona

country: Spain

institute: Sequentia Biotech SL.

data_processing:
Raw FASTQ files were pre-processed according to standard QC procedures like filtering high-quality reads by means of FastQC and BBDuk  (Bushnell et al. 2017). Minimum read length and minimum Phred-quality score were set to 35 bp and a score of 25 respectively. After, reads were mapped againts the human genome (GRCh38/Ensembl release 104) and assigned to genes with with STARsolo (Kaminow et al., 2021).
Assembly: hg38
Supplementary files format and content: Processed files were subjected to additional QC steps: genes with low and constant levels of counts across one or more cells were filtered out to remove “uninformative” genes. Filtered gene data was then used for cluster identification, cell-doublet identification, marker gene analysis, and cluster annotation.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embyronic

extract_protocol:
This process was performed following 10x genomics recommended guidelines
Libraries were constructed using single cell 3' GEM kit v3.1 and following manufacturer protocol

value: embyronic

value: postimplantation human blastoids + DMSO

value: mixed embyonic cells


title: PB_12wk_3x_3

description: Library name: PPP3_62

source_name: Primary Meristem

value: Primary Meristem


title: SB_12wk_3x_2

description: Library name: PPP3_61


title: Tumor-LepR-single positive-4

description:
Library name: Sample33
LepR-single positive replicate 4
LIB062306_TRA00279102_T-SP4-LEPR_S7

value: Tumor

value: LepR-single positive CD8 T cells


title: Tumor-CD36-LepR-double positive-2

description:
Library name: Sample35
CD36-LepR-double positive replicate 2
LIB062306_TRA00279105_T-DP2-36_LEPR_S9

value: WT mice

value: CD36-LepR-double positive CD8 T cells


title: PB_12wk_3x_2

description: Library name: PPP3_60


title: P5, replicate 1, scRNAseq


title: Tumor-LepR-single positive-3

description:
Library name: Sample32
LepR-single positive replicate 3
LIB062306_TRA00279101_T-SP3-LEPR_S6


title: Separately_housed_WT_Rep3_aorta

description:
Library name: AOF106
Raw counts_aorta.csv


title: Single-nucleus sequencing of rice at the flowering stage of the node

description: Library name: RNA2

value: at the flowering stage of the node

value: nuclei

value: WT


title: Separately_housed_WT_Rep2_aorta

description:
Library name: AOF105
Raw counts_aorta.csv


title: Human PBMCs_2

city: Shanghai

first: Yibo

last: Zhang

address: 131 Dongan Road, Xuhui District, Shanghai

department: Institutes of Biomedical Sciences

institute: Fudan University

description: 10× Genomics

data_processing:
Cutadapt (version 1.9.1) was used to perform data volume and sequencing quality statistics on the original sequencing data.Cell Ranger software(v7.1.0) was used for basic analysis of sequencing data, including removing reads with low sequencing quality, obtaining unfiltered feature-barcode matrix and quantitative results of cell-gene expression.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values and matrix files

source_name: Human peripheral blood mononuclear cells

extract_protocol:
1μg/ml CD3 and CD28 were used to activate Human PBMCs after thawing them. The control group was added to PBS for 4h, and the experimental group was treated with the same amount of ITPRIPL1-ECD-Fc for 4h. Then prepared single-cell suspensions and measured cell viability.
Gel beads containing Barcode information are mixed with a mixture of samples and enzymes using the 10x Genomics and then coated with droplets of oil surfactants located in the Chromium system to form GEMs(Gel Beads in-Emulsions). In GEMs, Gel beads will release primers containing Illumina TruSeq Read1, 10x Barcode, UMI and Poly(dT), and bind with mRNA released after cell lysis to form full-length cDNA with Barcode label through reverse transcription. cDNA in GEMs was recovered and amplified by PCR. Then the cDNA fragment length was optimized by enzyme digestion and fragment screening. Finally, the construction process was completed through terminal repair and the traditional second-generation sequencing connector, and the standard sequencing DNA library was amplified by PCR.

value: ITPRIPL1-ECD-Fc 4h


title: Tumor-LepR-single positive-2

description:
Library name: Sample31
LepR-single positive replicate 2
LIB062306_TRA00279100_T-SP2-LEPR_S5


title: DMSO_D6

value: preimplantation human blastoids + DMSO


title: SB_12wk_3x_1

description: Library name: PPP3_59


title: Tumor-LepR-single positive-1

description:
Library name: Sample30
LepR-single positive replicate 1
LIB062306_TRA00279099_T-SP1-LEPR_S4


title: PB_12wk_3x_1

description: Library name: PPP3_58


title: Separately_housed_WT_Rep1_aorta

description:
Library name: AOF104
Raw counts_aorta.csv

value: aorta


title: SB_12wk_2x_3

description: Library name: PPP3_57


title: pH7.4 RNAseq 1

city: THUWAL

first: Samhan

middle: M.

last: Alsolami

address: Thuwal 23955

department: BESE

country: Saudi Arabia

institute: KAUST

data_processing:
NOT PROVIDED; REQUESTED
Assembly: NOT PROVIDED; REQUESTED
Supplementary files format and content: bed file
Supplementary files format and content: FPKM file

source_name: transformed

extract_protocol:
ATAC-seq: We've used Diagenade kit
RNA-seq: We've used RNeasy kit
ATAC-seq: Followed Diagenade kit instruction
RNA-seq: Followed  kit instruction

value: transformed

value: human B lymphoblastoid cells (LCL)


title: pH7.4 RNAseq 2


title: PB_12wk_2x_3

description: Library name: PPP3_56

value: Russet Burbank (Solanum tuberosum L.)


title: Separately_housed_KO_Rep_5_Ileum

description:
Library name: FI5
Raw counts_ileum.csv

source_name: Ileum

value: Ileum


title: Separately_housed_KO_Rep_4_Ileum

description:
Library name: FI4
Raw counts_ileum.csv


title: Tumor-CD36-LepR-double negative-2

description:
Library name: Sample28
CD36-LepR-double negative repliacte 2
LIB062306_TRA00279097_T-DN3-36_LEPR_S2

value: CD36-LepR-double negative CD8 T cells


title: Human PBMCs_1

description: 10× Genomics

value: Human peripheral blood mononuclear cells

value: PBS-treatment 4h


title: CTRL RNAseq 2

value: CTRL


title: PB_12wk_2x_2

description: Library name: PPP3_54

value: Primary Meristem


title: Tumor-CD36-LepR-double negative-1

description:
Library name: Sample27
CD36-LepR-double negative repliacte 1
LIB062306_TRA00279096_T-DN2-36_LEPR_S1

value: Tumor

value: WT mice


title: pH6.8 RNAseq 2


title: Separately_housed_KO_Rep_2_Ileum

description:
Library name: MI5
Raw counts_ileum.csv


title: SB_12wk_2x_2

description: Library name: PPP3_55

value: Secondary Meristem


title: pH6.8 RNAseq 1


title: Tumor-CD36-LepR-double negative-3

description:
Library name: Sample29
CD36-LepR-double negative repliacte 3
LIB062306_TRA00279098_T-DN4-36_LEPR_S3


title: Separately_housed_KO_Rep_3_Ileum

description:
Library name: MI6
Raw counts_ileum.csv


title: CTRL RNAseq 1


title: Tumor-TagBFP-GFP-DP-3

description:
Library name: Sample24
Tumor-TagBFP-GFP-double positive-3
LIB060355_TRA00265852_T4-DP_S18

value: IFNg-CyCLoPs mice

value: TagBFP-GFP-double positive CD8 T cells


title: Tumor-TagBFP-GFP-DP-5

description:
Library name: Sample26
Tumor-TagBFP-GFP-double positive-5
LIB060355_TRA00265858_T6-DP_S24


title: Separately_housed_KO_Rep_6_Ileum

description:
Library name: FI6
Raw counts_ileum.csv


title: Separately_housed_KO_Rep_1_Ileum

description:
Library name: MI4
Raw counts_ileum.csv


title: Tumor-TagBFP-GFP-DP-4

description:
Library name: Sample25
Tumor-TagBFP-GFP-double positive-4
LIB060355_TRA00265855_T5-DP_S21


title: SB_12wk_2x_1

description: Library name: PPP3_53


title: pH7.4 ATACseq 2

value: WT


title: Separately_housed_WT_Rep_6_Ileum

description:
Library name: FI3
Raw counts_ileum.csv


title: PB_12wk_2x_1

description: Library name: PPP3_52


title: PB_12wk_1x_3

description: Library name: PPP3_50


title: Separately_housed_WT_Rep_5_Ileum

description:
Library name: FI2
Raw counts_ileum.csv


title: pH7.4 ATACseq 1


title: Separately_housed_WT_Rep_4_Ileum

description:
Library name: FI1
Raw counts_ileum.csv


title: pH6.8 ATACseq 2


title: Tumor-TagBFP-SP-5

description:
Library name: Sample20
Tumor-TagBFP-single positive replicate 5
LIB060355_TRA00265854_T5-B_S20

value: TagBFP-single positive CD8 T cells


title: Tumor-TagBFP-GFP-DP-1

description:
Library name: Sample22
Tumor-TagBFP-GFP-double positive-1
LIB060355_TRA00265844_T1-DP_S10


title: SB_12wk_1x_2

description: Library name: PPP3_49


title: Separately_housed_WT_Rep_3_Ileum

description:
Library name: MI3
Raw counts_ileum.csv


title: SB_12wk_1x_3

description: Library name: PPP3_51


title: Separately_housed_WT_Rep_1_Ileum

description:
Library name: MI1
Raw counts_ileum.csv


title: Tumor-TagBFP-SP-6

description:
Library name: Sample21
Tumor-TagBFP-single positive replicate 6
LIB060355_TRA00265857_T6-B_S23


title: pH6.8 ATACseq 1


title: SB_12wk_1x_1

description: Library name: PPP3_47


title: Tumor-TagBFP-GFP-DP-2

description:
Library name: Sample23
Tumor-TagBFP-GFP-double positive-2
LIB060355_TRA00265847_T2-DP_S13


title: Tumor-TagBFP-SP-4

description:
Library name: Sample19
Tumor-TagBFP-single positive replicate 4
LIB060355_TRA00265851_T4-B_S17


title: CTRL ATACseq 1


title: PB_12wk_1x_2

description: Library name: PPP3_48


title: Tumor-TagBFP-SP-3

description:
Library name: Sample18
Tumor-TagBFP-single positive replicate 3
LIB060355_TRA00265849_T3-B_S15


title: CTRL ATACseq 2


title: Separately_housed_WT_Rep_2_Ileum

description:
Library name: MI2
Raw counts_ileum.csv


title: CUT&Tag anti-YY1 of mouse microglia, MCAO day 28, Cx3cr1-CreER;Zfp384flox/flox

description:
Library name: CutTag_Day28_cKO_YY1
CUT&Tag with anti-YY1 antibody (Abcam, ab109237) on FACS-sorted CD45(int)CD11b(int) microglia from Cx3cr1-CreER;Zfp384flox/flox mouse brain on day 28 after stroke onset. Sequenced on Illumina HiSeq 2500 (PE150).

data_processing:
Reads were mapped to the mm10 (genome file) by Bowtie2, as for ATAC-seq.
Duplicate reads were removed with picard-tools-1.119.
For primary microglia samples, peaks were called with SEACR. Peaks with only one unique read count were then removed. For BV2 cell line samples, peaks were called with MACS2 (narrowPeak).
Signal tracks were plotted by deepTools. BigWig files were generated for visualization.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BigWig signal track files.
Library strategy: CUT&Tag

growth_protocol: All mice were maintained in a conventional facility at the Institute of Science Tokyo or Tokyo Metropolitan Institute of Medical Science in Tokyo, Japan. All experiments were approved by the Institutional Animal Research Committee of the Institute of Science Tokyo (approval number: A2025-011C2) and Tokyo Metropolitan Institute of Medical Science (approval number: 21-004). C57BL/6J mice were used for WT mice. BV2, a microglial cell line, was supplied by Prof. Kazuhide Inoue at Kyushu University, Japan.

extract_protocol:
For primary microglia: Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). CD45(int)CD11b(int) cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific). For BV2 cells: BV2 cells were harvested from culture.
CUT&Tag libraries were prepared using a bench top CUT&Tag V.2 protocol with slight modifications, as described previously (Nakamura et al., Neuron 2023). BV2 cells or CD45(int)CD11b(int) cells (100,000–200,000 cells from the sham-operated or ischemic hemisphere) were pelleted for 3 min at 600×g at room temperature. Anti-YY1 (Abcam, ab109237) and anti-ZNF384 (Sigma, HPA004051) antibodies were used for primary antibodies. Sequencing was performed using the PE150 strategy on Illumina HiSeq 2500 for primary microglia and BV2 IgG samples, or Illumina NovaSeq 6000 for BV2 anti-ZFP384 and anti-YY1 antibody samples.

value: brain

value: microglia

value: Zfp384 cKO (DBD deletion) (Cx3cr1-CreER; Zfp384 flox/flox)

value: MCAO


title: Tumor-TagBFP-SP-2

description:
Library name: Sample17
Tumor-TagBFP-single positive replicate 2
LIB060355_TRA00265846_T2-B_S12


title: SB_12wk_Ctrl_3

description: Library name: PPP3_45

value: Russet Burbank (Solanum tuberosum L.)

value: Control


title: CUT&Tag IgG control of mouse microglia, MCAO day 28, Cx3cr1-CreER;Zfp384flox/flox

description:
Library name: CutTag_Day28_cKO_IgG
CUT&Tag with IgG control antibody on FACS-sorted CD45(int)CD11b(int) microglia from Cx3cr1-CreER;Zfp384flox/flox mouse brain on day 28 after stroke onset. Sequenced on Illumina HiSeq 2500 (PE150).


title: Tumor-TagBFP-SP-1

description:
Library name: Sample16
Tumor-TagBFP-single positive replicate 1
LIB060355_TRA00265843_T1-B_S9


title: PB_12wk_Ctrl_3

description: Library name: PPP3_44


title: Blood_Control_Short Read 49

city: Boca Raton

first: Massimo

last: Caputi

address: 777 Glades Road

institute: Florida Atlantic University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through customperl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and lowquality readsfrom raw data. At the same time, Q20, Q30, and GC-content of the rawdatawere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression anddistribution on the reference.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Assembly: ensembl_82_homo_sapiens_grch38_primary
Supplementary files format and content: sRNA_ADvsControl.Differential_analysis_results.xlsx; differential expression

source_name: Whole Blood

extract_protocol:
The blood was collected in PAXgene Blood RNA tubes. Total RNA was extracted following the protocol developed by this lab to isolate RNAs of different sizes and low concentration (Paz S, Mauer C, Ritchie A, Robishaw JD, Caputi M. A simplified SARS-CoV-2 detection protocol for research laboratories. PLoS One. 2020 Dec 18;15(12):e0244271). RNA sample quality and quantity were determined utilizing an Agilent TapeStation system and a NanoDrop spectrophotometer. The samples utilized for the cDNA library preparations had an RNA integrity number (RIN) ≥ 7 and an RNA concentration ≥ 30 ng/µL. Ribosomal RNA was removed by Epicentre TruSeq Stranded Total RNA Library Prep Gold/illumina/20020599
A total amount of 2 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina and index (X) primer. PCR products were purified on an 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

value: Whole Blood


title: PB_12wk_1x_1

description: Library name: PPP3_46


title: CUT&Tag IgG control of mouse microglia, MCAO day 28, Zfp384flox/flox control

description:
Library name: CutTag_Day28_Control_IgG
CUT&Tag with IgG control antibody on FACS-sorted CD45(int)CD11b(int) microglia from Zfp384flox/flox mouse brain on day 28 after stroke onset. Sequenced on Illumina HiSeq 2500 (PE150).


title: SB_12wk_Ctrl_2

description: Library name: PPP3_43


title: mLN-TagBFP-SP-3

description:
Library name: Sample15
mLN-TagBFP-single positive replicate 3
LIB060355_TRA00265841_mLN3_S7

source_name: mLN

value: mLN


title: Blood_Control_Short Read 46


title: mLN-TagBFP-SP-2

description:
Library name: Sample14
mLN-TagBFP-single positive replicate 2
LIB060355_TRA00265840_mLN2_S6


title: CUT&Tag IgG control of mouse microglia, MCAO day 6

description:
Library name: CutTag_Day6_IgG
CUT&Tag with IgG control antibody on FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 6 after stroke onset. Sequenced on Illumina HiSeq 2500 (PE150).

source_name: brain

value: wild-type


title: Blood_Control_Short Read 45


title: PB_12wk_Ctrl_2

description: Library name: PPP3_42

value: Primary Meristem


title: CUT&Tag anti-YY1 of mouse microglia, MCAO day 28, Zfp384flox/flox control

description:
Library name: CutTag_Day28_Control_YY1
CUT&Tag with anti-YY1 antibody (Abcam, ab109237) on FACS-sorted CD45(int)CD11b(int) microglia from Zfp384flox/flox mouse brain on day 28 after stroke onset. Sequenced on Illumina HiSeq 2500 (PE150).


title: SB_12wk_Ctrl_1

description: Library name: PPP3_41


title: mLN-TagBFP-SP-1

description:
Library name: Sample13
mLN-TagBFP-single positive replicate 1
LIB060355_TRA00265839_mLN1_S5


title: Blood_Control_Short Read 48


title: PB_12wk_Ctrl_1

description: Library name: PPP3_40


title: Blood_Control_Short Read 44


title: Blood_Control_Short Read 43


title: spleen-TagBFP-SP-4

description:
Library name: Sample12
spleen-TagBFP-single positive replicate 4
LIB060355_TRA00265838_Sp4_S4

source_name: spleen

value: spleen


title: Blood_Control_Short Read 47


title: PB_9wk_2x_3

description: Library name: PPP3_38


title: CUT&Tag anti-YY1 of mouse microglia, sham surgery

description:
Library name: CutTag_Sham_YY1
CUT&Tag with anti-YY1 antibody (Abcam, ab109237) on FACS-sorted CD45(int)CD11b(int) microglia from sham-operated mouse brain. Sequenced on Illumina HiSeq 2500 (PE150).

value: Sham surgery


title: CUT&Tag IgG control of BV2 microglial cell line

description:
Library name: CutTag_BV2_IgG
CUT&Tag with IgG control antibody in BV2 microglial cell line. Sequenced on Illumina HiSeq 2500 (PE150).

source_name: BV2 microglial cell line

value: BV2 microglial cell line

value: untreated


title: SB_9wk_2x_3

description: Library name: PPP3_39

value: Secondary Meristem


title: Blood_Control_Short Read 42


title: CUT&Tag anti-YY1 of mouse microglia, MCAO day 6

description:
Library name: CutTag_Day6_YY1
CUT&Tag with anti-YY1 antibody (Abcam, ab109237) on FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 6 after stroke onset. Sequenced on Illumina HiSeq 2500 (PE150).


title: Blood_Control_Short Read 41


title: spleen-TagBFP-SP-2

description:
Library name: Sample10
spleen-TagBFP-single positive replicate 2
LIB060355_TRA00265836_Sp2_S2

value: IFNg-CyCLoPs mice


title: CUT&Tag IgG control of mouse microglia, sham surgery

description:
Library name: CutTag_Sham_IgG
CUT&Tag with IgG control antibody on FACS-sorted CD45(int)CD11b(int) microglia from sham-operated mouse brain. Sequenced on Illumina HiSeq 2500 (PE150).


title: spleen-TagBFP-SP-1

description:
Library name: Sample9
spleen-TagBFP-single positive replicate 1
LIB060355_TRA00265835_Sp1_S1

value: TagBFP-single positive CD8 T cells


title: spleen-TagBFP-SP-3

description:
Library name: Sample11
spleen-TagBFP-single positive replicate 3
LIB060355_TRA00265837_Sp3_S3


title: RNA-seq of mouse microglia, MCAO day 6, Cx3cr1-CreER;Yy1flox/flox replicate 3

description:
Library name: bulkRNA_Day06_Yy1cKO_Rep3
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from Cx3cr1-CreER;Yy1flox/flox mouse brain on day 6 after stroke onset (biological replicate 3). Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_Yy1_gene_counts.txt

data_processing:
Reads were aligned to the mm10 annotation file using STAR, and the read counts for each gene were determined through featureCounts.
Normalization and differential expression analysis were performed using edgeR. DEGs were identified by edgeR.
Gene ontology analysis was performed using DAVID (https://david.ncifcrf.gov/).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text file containing gene-level raw counts (rows: genes, columns: samples).

extract_protocol:
Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). The cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific).
Total RNA was purified using a RNeasy micro kit (Qiagen) and used for the preparation of RNA-seq libraries by an Ovation SoLo RNA-Seq Library Preparation Kit (Tecan), according to the manufacturer's procedure. Following the assessment of quantity and fragment size distribution of cDNA libraries by Agilent TapeStation 4150, the libraries were sequenced by Illumina HiSeq 2500. Libraries for the Day 14 Igf1 cohort were sequenced on Illumina NovaSeq 6000.

value: brain


title: SB_9wk_2x_2

description: Library name: PPP3_37


title: IEC-GFP-High-4

description:
Library name: Sample8
GFP high cell replicate 4
LIB060842_TRA00267775_IEC-GFP-High-4_S17

source_name: ileum

value: ileum

value: IL-17A-CyCLoPs mice

value: GFP high IEC


title: PB_9wk_2x_2

description: Library name: PPP3_36

value: Russet Burbank (Solanum tuberosum L.)


title: RNA-seq of mouse microglia, MCAO day 6, Cx3cr1-CreER;Yy1flox/flox replicate 2

description:
Library name: bulkRNA_Day06_Yy1cKO_Rep2
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from Cx3cr1-CreER;Yy1flox/flox mouse brain on day 6 after stroke onset (biological replicate 2). Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_Yy1_gene_counts.txt

value: microglia

value: MCAO


title: Blood_Control_Short Read 40

value: Whole Blood

value: Control


title: Blood_Control_Short Read 39


title: RNA-seq of mouse microglia, MCAO day 6, Cx3cr1-CreER;Yy1flox/flox replicate 1

description:
Library name: bulkRNA_Day06_Yy1cKO_Rep1
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from Cx3cr1-CreER;Yy1flox/flox mouse brain on day 6 after stroke onset (biological replicate 1). Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_Yy1_gene_counts.txt


title: Blood_Control_Short Read 38


title: IEC-GFP-High-3

description:
Library name: Sample7
GFP high cell replicate 3
LIB060842_TRA00267770_IEC-GFP-High-3_S12


title: PB_9wk_2x_1

description: Library name: PPP3_34

value: Primary Meristem


title: Blood_Control_Short Read 37


title: IEC-GFP-High-2

description:
Library name: Sample6
GFP high cell replicate 2
LIB060842_TRA00267765_IEC-GFP-High-2_S8


title: RNA-seq of mouse microglia, MCAO day 6, Yy1flox/flox control replicate 3

description:
Library name: bulkRNA_Day06_Yy1flox_Rep3
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from Yy1flox/flox mouse brain on day 6 after stroke onset (biological replicate 3). Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_Yy1_gene_counts.txt


title: SB_9wk_1x_3

description: Library name: PPP3_33


title: IEC-GFP-High-1

description:
Library name: Sample5
GFP high cell replicate 1
LIB060842_TRA00267760_IEC-GFP-High-1_S3


title: Blood_Control_Short Read 36


title: Blood_Control_Short Read 35


title: PB_9wk_1x_3

description: Library name: PPP3_32


title: SB_9wk_1x_2

description: Library name: PPP3_31


title: IEC-GFP-Neg-4

description:
Library name: Sample4
GFP negative cell replicate 4
LIB060842_TRA00267773_IEC-GFP-Neg-4_S15

value: GFP negative IEC


title: IEC-GFP-Neg-3

description:
Library name: Sample3
GFP negative cell replicate 3
LIB060842_TRA00267768_IEC-GFP-Neg-3_S10


title: RNA-seq of mouse microglia, MCAO day 6, Yy1flox/flox control replicate 1

description:
Library name: bulkRNA_Day06_Yy1flox_Rep1
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from Yy1flox/flox mouse brain on day 6 after stroke onset (biological replicate 1). Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_Yy1_gene_counts.txt


title: RNA-seq of mouse microglia, MCAO day 6, Igf1-Egfp EGFP+

description:
Library name: bulkRNA_Day06_Igf1pos
RNA-seq of FACS-sorted CD45(int)CD11b(int) EGFP+ microglia from Igf1-Egfp transgenic mouse brain on day 6 after stroke onset. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt

value: MCAO (Igf1-EGFP positive)


title: SB_9wk_2x_1

description: Library name: PPP3_35


title: IEC-GFP-Neg-2

description:
Library name: Sample2
GFP negative cell replicate 2
LIB060842_TRA00267763_IEC-GFP-Neg-2_S6


title: RNA-seq of mouse microglia, MCAO day 28, wild-type

description:
Library name: bulkRNA_Day28_WT
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 28 after stroke onset. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt

value: wild-type


title: IEC-GFP-Neg-1

description:
Library name: Sample1
GFP negative cell replicate 1
LIB060842_TRA00267758_IEC-GFP-Neg-1_S1


title: Blood_Control_Short Read 32


title: RNA-seq of mouse microglia, MCAO day 6, Yy1flox/flox control replicate 2

description:
Library name: bulkRNA_Day06_Yy1flox_Rep2
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from Yy1flox/flox mouse brain on day 6 after stroke onset (biological replicate 2). Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_Yy1_gene_counts.txt


title: SB_9wk_1x_1

description: Library name: PPP3_29


title: Blood_Control_Short Read 34


title: UPEC Testis Tam only control Rep 3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: Library name: UPEC_Testis_TamOnly_3

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific reads was done using nf-core RNA-seq pipeline v3.7
Normalization and detection of differentially expressed genes was performed using DESeq2 (v1.42.0)
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

source_name: Testis

extract_protocol:
RNA was extracted from testis, proximal (segment 1-5) and distal epididymis (segment 6-10) using the RNeasy Mini Kit (Qiagen) after bead-based tissue homogenization (Tissue homogenizer Retsch, 2.8 mm stainless steel beads)
RNA-seq

value: Testis

value: Tamoxifen only


title: SB_9wk_Ctrl_2

description: Library name: PPP3_27

value: Secondary Meristem


title: UPEC Testis Tam only control Rep 2

description: Library name: UPEC_Testis_TamOnly_2


title: Blood_Control_Short Read 31


title: PB_9wk_Ctrl_3

description: Library name: PPP3_26


title: RNA-seq of mouse microglia, MCAO day 1, wild-type

city: Yushima, Bunkyo-ku

first: Jun

last: Tsuyama

institute: Institute of Science Tokyo

description:
Library name: bulkRNA_Day01_WT
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 1 after stroke onset. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt


title: Blood_Control_Short Read 33


title: UPEC Testis Tam only control Rep 1

description: Library name: UPEC_Testis_TamOnly_1


title: Blood_Control_Short Read 30


title: RNA-seq of mouse microglia, MCAO day 6, Igf1-Egfp EGFP–

description:
Library name: bulkRNA_Day06_Igf1neg
RNA-seq of FACS-sorted CD45(int)CD11b(int) EGFP– microglia from Igf1-Egfp transgenic mouse brain on day 6 after stroke onset. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt

value: MCAO (Igf1-EGFP negative)


title: Blood_Control_Short Read 29


title: PB_9wk_1x_1

description: Library name: PPP3_28


title: Blood_Control_Short Read 28


title: PB_9wk_1x_2

description: Library name: PPP3_30


title: RNA-seq of mouse microglia, sham surgery, wild-type

description:
Library name: bulkRNA_Sham_WT
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from sham-operated mouse brain. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt

value: brain

value: Sham surgery


title: RNA-seq of mouse microglia, MCAO day 14, wild-type

description:
Library name: bulkRNA_Day14_WT
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 14 after stroke onset. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt


title: RNA-seq of mouse microglia, MCAO day 6, wild-type

description:
Library name: bulkRNA_Day06_WT
RNA-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 6 after stroke onset. Libraries were sequenced by Illumina HiSeq 2500.
bulkRNA_timeseries_Day6Igf1_gene_counts.txt


title: PB_9wk_Ctrl_2

description: Library name: PPP3_24


title: UPEC Testis Tam+Dtx Rep 2

description: Library name: UPEC_Testis_TamDtx_2

value: Tamoxifen + Diphtheria toxin


title: SB_9wk_Ctrl_1

description: Library name: PPP3_25


title: PB_9wk_Ctrl_1

description: Library name: PPP3_22


title: Blood_Control_Short Read 27


title: UPEC Testis Tam+Dtx Rep 1

description: Library name: UPEC_Testis_TamDtx_1


title: UPEC Testis Tam+Dtx Rep 3

description: Library name: UPEC_Testis_TamDtx_3


title: ATAC-seq of mouse microglia, MCAO day 28, wild-type

description:
Library name: ATAC_Day28_WT
ATAC-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 28 after stroke onset. Libraries were sequenced using the Illumina HiSeq 2500.

data_processing:
Reads were mapped to mm10 (genome file) by Bowtie2.
ATAC-seq signal peaks were detected by MACS2 default parameters.
BigWig signal track files were generated using deepTools bamCoverage with RPGC normalization.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BigWig signal track files (RPGC-normalized coverage).

extract_protocol:
Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). The cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific).
An ATAC-seq library was prepared according to the protocol described previously (Nakamura et al., Neuron 2023). For the fragmentation and tagmentation of genomic DNA, 50,000 nuclei isolated from CD45(int)CD11b(int) cells were treated with Tn5 transposase (Illumina, Nextera DNA Library Preparation Kit). The DNA fragments were amplified using KAPA HiFi HS ReadyMix (Kapa Biosystems) and purified using SPRI select beads (Beckman). Library quality and fragment size distribution were assessed by Agilent TapeStation 4150. Libraries were sequenced using the Illumina HiSeq 2500 for wild-type time-course samples or Illumina NovaSeq 6000 for Igf1-CreER;Ai14 samples.


title: ATAC-seq of mouse microglia, MCAO day 14, wild-type

description:
Library name: ATAC_Day14_WT
ATAC-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 14 after stroke onset. Libraries were sequenced using the Illumina HiSeq 2500.


title: Blood_Control_Short Read 26


title: ATAC-seq of mouse microglia, MCAO day 6, wild-type

description:
Library name: ATAC_Day06_WT
ATAC-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 6 after stroke onset. Libraries were sequenced using the Illumina HiSeq 2500.


title: SB_6wk_1x_2

description: Library name: PPP3_21


title: UPEC Proximal regions Tam only control Rep 3

description: Library name: UPEC_ProxEpi_TamOnly_3

source_name: proximal epididymis (IS+Caput)

value: proximal epididymis (IS+Caput)


title: Blood_Control_Short Read 25


title: PB_6wk_1x_3

description: Library name: PPP3_20

value: Russet Burbank (Solanum tuberosum L.)


title: Blood_Control_Short Read 24


title: ATAC-seq of mouse microglia, MCAO day 1, wild-type

description:
Library name: ATAC_Day01_WT
ATAC-seq of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 1 after stroke onset. Libraries were sequenced using the Illumina HiSeq 2500.

value: microglia


title: UPEC Proximal regions Tam only control Rep 2

description: Library name: UPEC_ProxEpi_TamOnly_2


title: SB_6wk_1x_1

description: Library name: PPP3_19


title: Blood_Control_Short Read 23


title: UPEC Proximal regions Tam only control Rep 1

description: Library name: UPEC_ProxEpi_TamOnly_1


title: ATAC-seq of mouse microglia, sham surgery, wild-type

description:
Library name: ATAC_Sham_WT
ATAC-seq of FACS-sorted CD45(int)CD11b(int) microglia from sham-operated mouse brain. Libraries were sequenced using the Illumina HiSeq 2500.


title: Blood_Control_Short Read 22


title: UPEC Proximal regions Tam+Dtx Rep 2

description: Library name: UPEC_ProxEpi_TamDtx_2


title: Blood_Control_Short Read 21


title: PB_6wk_1x_1

description: Library name: PPP3_16


title: UPEC Proximal regions Tam+Dtx Rep 3

description: Library name: UPEC_ProxEpi_TamDtx_3


title: SB_6wk_Ctrl_3

description: Library name: PPP3_15


title: BALB/c_16wk_LG_biol rep 2

city: Boston

first: Danny

last: Toribio

address: One Kneeland St

department: Basic and Clinical Translational Sciences

institute: Tufts University School of Dental Medicine

description: Library name: 16Week_BABL_c2

data_processing:
Basecalling and demultiplexing were performed on the raw sequence data using Illumina's bcl2fastq software.
Quality control of the read data was conducted using the FastQC tool.
Sequencing reads from the compressed fastq files were mapped to the mouse reference genome (mm10) using the HISAT2 alignment program.
Raw gene count tables were generated from the resulting alignment files and the mm10 gene annotation files using the featureCounts program from the Rsubread package.
Assembly: mouse reference genome (mm10)
Supplementary files format and content: tab-delimited-value text file with raw count of each sample

source_name: Exorbital Lacrimal Gland

extract_protocol:
Excised lacrimal glands were placed in RNAlater stabilization solution (Thermo Fisher Scientific, Waltham, MA) for storage at -20˚C prior to RNA extraction. Total RNA was extracted and purified using the RNeasy Midi Kit (Qiagen, Germantown, MD) following the manufacturer's instructions. Purified RNA samples were stored at -80°C until downstream use.
100 - 200 ng of total RNA was used for the construction of the sequencing libraries using the Illumina TruSeq stranded mRNA kit, as per the manufacturer’s instructions. The resulted libraries were then analyzed on an Agilent Fragment Analyzer for molar quantification and size distribution, and then pooled at equal molar for sequencing on an Illumina HiSeq 2500 sequencer using V4 chemistry and single read 50 bases format.

value: Exorbital Lacrimal Gland

value: BALB/cJ


title: Blood_Control_Short Read 20

value: Whole Blood

value: Control


title: PB_6wk_Ctrl_3

description: Library name: PPP3_14

value: Primary Meristem


title: BALB/c_8wk_LG_biol rep 3

description: Library name: 8Week_BABL_c3


title: SB_6wk_Ctrl_2

description: Library name: PPP3_13


title: UPEC Distal regions Tam only Rep 2

description: Library name: UPEC_DisEpi_TamOnly_2

source_name: distal epididymis (Corpus+Cauda)

value: distal epididymis (Corpus+Cauda)


title: Blood_Control_Short Read 19


title: Blood_Control_Short Read 18


title: BALB/c_16wk_LG_biol rep 3

description: Library name: 16Week_BABL_c3


title: UPEC Distal regions Tam only Rep 1

description: Library name: UPEC_DisEpi_TamOnly_1


title: BALB/c_8wk_LG_biol rep 1

description: Library name: 8Week_BABL_c1


title: PB_6wk_1x_2

description: Library name: PPP3_18


title: BALB/c_16wk_LG_biol rep 1

description: Library name: 16Week_BABL_c1


title: UPEC Distal regions Tam+Dtx Rep 3

description: Library name: UPEC_DisEpi_TamDtx_3


title: UPEC Proximal regions Tam+Dtx Rep 1

description: Library name: UPEC_ProxEpi_TamDtx_1


title: Blood_Control_Short Read 17


title: PB_6wk_Ctrl_2

description: Library name: PPP3_12


title: UPEC Distal regions Tam+Dtx Rep 2

description: Library name: UPEC_DisEpi_TamDtx_2


title: BALB/c_8wk_LG_biol rep 2

description: Library name: 8Week_BABL_c2


title: Blood_Control_Short Read 16


title: UPEC Distal regions Tam only Rep 3

description: Library name: UPEC_DisEpi_TamOnly_3


title: PB_6wk_Ctrl_1

description: Library name: PPP3_10


title: PB_3wk_1x_3

description: Library name: PPP3_9


title: Blood_Control_Short Read 15


title: BALB/c_3wk_LG_biol rep 2

description: Library name: 3Week_BABL_c2


title: Blood_Control_Short Read 14


title: SB_6wk_Ctrl_1

description: Library name: PPP3_11


title: NOD_16wk_LG_biol rep 3

description: Library name: 16Week_NOD3

value: NOR/LtJ


title: BALB/c_3wk_LG_biol rep 1

description: Library name: 3Week_BABL_c1


title: macrophages, ZM-3

city: Guangzhou

first: Shuo

last: Shi

state: Guangdong Province

address: No.1023, South Shatai Road Baiyun District

department: School of Basic Medical Sciences

institute: Southern Medical University

description: Library name: Smaple 6

data_processing:
Fastp v0.23.2, Hisat2 v2.2.1, FeatureCounts v2.0.3, and DESeq2 (R package v1.34.0) were used for data processing.
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html) , DEGs with \(|log 2 FC|>1\) and \(Padj <0.05\) were considered to be significantly different expressed genes.
Assembly: mm10
Supplementary files format and content: tab - delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: bone marrow

growth_protocol: BMMs were generated from the bone marrow of 6-week-old C57BL/6 male mice as described previously. The bone marrow cells were then obtained by flushing the bones with a 1 mL syringe. Subsequently, the cells were suspended in α-MEM complete medium supplemented with 10% fetal bovine serum and 30 ng/mL M-CSF. The cells were cultured at 37 ℃ in a 5% CO2 incubator. After three days, the adherent cells were identified as bone marrow-derived macrophages.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Cat.9109, Takara Biotechnology), following the manufacturer’s instructions and using three samples per group. RNA concentration and purity were quantified using a UV spectrophotometer (NanoDropOne, Thermo Fisher Scientific, USA).
RNA libraries for RNA - seq were prepared using ABclonal mRNA - seq Lib Prep Kit following the manufacturer’s protocols.

treatment_protocol: RNA-seq profiling was performed on bone marrow-derived macrophages (osteoclast precursor cells, induced for osteoclast differentiation). The cells were cultured in a complete α-MEM medium containing 10% FBS, supplemented with 30 ng/mL M-CSF and 100 ng/mL RANKL (key factors for osteoclast differentiation); those treated without 10 μM ZM served as the control group, and those treated with 10 μM ZM were the intervention group.

value: bone marrow

value: primary cell

value: bone marrow-derived macrophages

value: WT

value: complete α-MEM + 10% FBS + 30 ng/mL M-CSF + 100 ng/mL RANKL（with 10 μM ZM）

value: batch 1


title: PB_3wk_1x_1

description: Library name: PPP3_7


title: Blood_Control_Short Read 13


title: PB_3wk_1x_2

description: Library name: PPP3_8


title: macrophages, ZM-2

description: Library name: Smaple 5


title: NOD_16wk_LG_biol rep 2

description: Library name: 16Week_NOD2


title: BALB/c_3wk_LG_biol rep 3

description: Library name: 3Week_BABL_c3


title: Blood_Control_Short Read 12


title: NOD_16wk_LG_biol rep 1

description: Library name: 16Week_NOD1


title: PB_3wk_Ctrl_3

description: Library name: PPP3_6


title: macrophages, Ctrl-3

description: Library name: Smaple 3

value: complete α-MEM + 10% FBS + 30 ng/mL M-CSF + 100 ng/mL RANKL（without 10 μM ZM）


title: PB_3wk_Ctrl_2

description: Library name: PPP3_5