title: islets of PBKO mice

city: Jinan

first: Jia

last: Song

state: Select...

address: No.107 Wenhua Xi Road, Jinan,Shandong Province

institute: Qilu Hospital of Shandong University

description: Library name: K

library_source: genomic single cell

data_processing:
Raw sequencing data were converted to fastq format using ‘cellranger-atac mkfastq’ (10x Genomics, v.2.1.0). scATAC-seq reads were aligned to the GRCm38 (mm10) reference genome and quantified using ‘cellranger-atac count’ (10x Genomics, v.2.1.0).
Used iterative latent semantic indexing (LSI) approach to reduce the dimensionality of the sparse insertion counts matrix from many thousands to tens or hundreds.
Assembly: mm10
Supplementary files format and content: Fragments
Supplementary files format and content: .tar archives include peaks, matrix, and barcodes files.

source_name: islets

extract_protocol:
The islets of Brd4 conditional knockout (PBKO) and control mice were isolated using type XI collagenase and were dissociated using a trypsin EDTA solution for sequencing experiments.
Single cell suspension was loaded onto a microfluidic chip and single cell ATAC-seq libraries were constructed according to the manufacturer’s instructions.

value: islets

value: Brd4 conditional knockout


title: 7_neg_Ccr2Cre

status: Public on Mar 01 2026

type: SRA

city: Freiburg

first: Maximilian

last: Fliegauf

address: Breisacherstraße 113

department: Institute for Neuropathology

country: Germany

institute: Uniklinikum Freiburg

description:
Library name: S591_63_7_neg_S63_R1_001.fastq.gz
no_correction

library_source: transcriptomic

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17 software, which resulted in .bcl files, which were converted into fastq files with the bcl2fastq v2.20 software.
Bulk RNA-seq data was aligned with STAR v2.7.11a to the mouse reference genome Gencode M36. Counts were obtained using FeatureCounts v2.0.8. Data was analyzed using DESeq2 1.46.0.
Assembly: Gencode M36
Supplementary files format and content: Processed counts are provided in the files count_LPS_wildtype_GEO.txt, counts_Ccr2KO_GEO.txt, counts_LPS_Ccr2_GEO.txt for the respective genotypes

molecule: total RNA

organism: Mus musculus

source_name: Brain devoid of choroid plexuses

growth_protocol: SPF breeding facility

extract_protocol:
Cells were sorted into RNAprotect Cell Reagent (QIAGEN) according to the manufacturers recommendations. Total RNA was extracted from FACS sorted cells stabilized in RNAprotect Cell Reagent according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamination was removed by using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added, and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation with Illumina Nextera XT Sample Preparation. The sequencing run was performed on a HiSeq 1000 instrument (Control Software v2.2.68) using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

treatment_protocol: Mice were either treated with Vehicle solution (CTL) or with BLZ945 and each group with LPS or left untreated and injected with PBS. Ccr2CreERT2 R26tdT mice were treated with 2 mg tamoxifen at 0, 2 and 4 days after CTL or BLZ945 treatment. 8 weeks after the end of the treatment, mice were either left untreated or injected with LPS (CTL and BLZ945 groups). 12 hours later, mice were perfused and CAMs and MG were harvested.

tag: tissue

value: Brain devoid of choroid plexuses

tag: cell type

value: CAMs

tag: genotype

tag: treatment

tag: batch


title: islets of control mice

country: China

description: Library name: C

molecule: genomic DNA

value: control


title: 7_pos_Ccr2Cre

description:
Library name: S591_62_7_pos_S57_R1_001.fastq.gz
no_correction


title: 7_MG_Ccr2Cre

description:
Library name: S591_61_7_MG_S61_R1_001.fastq.gz
no_correction

value: MG


title: PBMC, PBSC, rep4

city: Stanford

first: Cameron

middle: Scott

last: Bader

state: California

address: 269 Campus Drive, CCSR Room 2250

department: BMT and Cell Therapy

country: USA

institute: Stanford University

description: Library name: R035

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned using STAR.
Assembly: GRCh38
Supplementary files format and content: Barcodes identify individual cells.
Supplementary files format and content: Features identify individual genes.
Supplementary files format and content: Matrices identify reads in sparse format.

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Cells were captured and lysed using the Fluent V3.0 PIPSeq platform.
Whole transcriptome libraries were generated according to manufactuer instructions.

treatment_protocol: Patients either received Orca-T immunotherapy or PBSC grafts ~3 weeks before PBMC isolation and capture.

value: PBMC

value: PBSC


title: 5_pos_Ccr2Cre

description:
Library name: S591_59_5_pos_S59_R1_001.fastq.gz
no_correction


title: 175_pos_Ccr2Cre

description:
Library name: S591_67_175_CAMs_pos_S67_R1_001.fastq.gz
no_correction


title: islets of dbR4 mice

description: Library name: DB4

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Assembly: Mus_musculus_ensembl_99
Supplementary files format and content: .tar archives include barcodes.tsv, genes.tsv, and matrix.mtx files.

molecule: polyA RNA

extract_protocol:
The islets of Db/db, Db/m, dbR2 and dbR4 mice were isolated using type XI collagenase and were dissociated using a trypsin EDTA solution for sequencing experiments.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

treatment_protocol: C57BLKS/J-Leprdb/Leprdb (db/db) and C57BLKS/J-Leprdb/m (db/m) male mice were used in this experiment. Male 5-week-old db/db mice were randomly assigned to an ad libitum diet with free access to regular chow (db/db-F), or receiving limited food supply (4g/day, R4; 2g/day, R2) for 1 month. Food was added for R4 and R2 mice at fixed time every day (12 o’clock). As control, male db/m mice were also given free access to regular chow (db/m-F) for 1 month. The islets of db/db, db/m,dbR2 and dbR4mice were subjected to scRNA-seq.

tag: Sex

value: male

tag: diet

value: limited food (4g/day)


title: 5_neg_Ccr2Cre

description:
Library name: S591_60_5_neg_S60_R1_001.fastq.gz
no_correction


title: PBMC, PBSC, rep3

description: Library name: R029


title: PBMC, OrcaT, rep4

description: Library name: R031

value: OrcaT


title: 1_neg_Ccr2Cre

description:
Library name: S591_57_1_neg_S62_R1_001.fastq.gz
no_correction


title: 5_MG_Ccr2Cre

description:
Library name: S591_58_5_MG_S58_R1_001.fastq.gz
no_correction


title: islets of Db/db mice

description: Library name: DBC

value: ad libitum diet


title: islets of Db/m mice

description: Library name: DBM


title: 1_MG_Ccr2Cre

description:
Library name: S591_55_1_MG_S55_R1_001.fastq.gz
no_correction


title: B4f_CAM

description:
Library name: S591_54_B4f_MG_S54_R1_001.fastq.gz
no_correction

value: Microglia

value: Ccr2 KO


title: 1_pos_Ccr2Cre

description:
Library name: S591_56_1_pos_S56_R1_001.fastq.gz
no_correction


title: B4f_MG

description:
Library name: S591_53_B4f_CAM_S53_R1_001.fastq.gz
no_correction


title: EO771-CSCs,replicate 3

city: Guangzhou

first: Qidong

last: Xia

state: Guangdong

address: No.107, Yangjiangxi Road, Guangzhou

department: Breast Tumor Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

description: Library name: Sample6

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 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: GRCm38.91
Supplementary files format and content: csv files include count values for each Sample

extract_protocol:
RNA was harvested using using Trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra Ⅱ RNA Library Prep kitfollowing manufacturer's protocols.

tag: cell line


title: PBMC, OrcaT, rep3

description: Library name: R020


title: PBMC, OrcaT, rep2

description: Library name: R019


title: islets of dbR2 mice

description: Library name: DB2

value: limited food (2g/day)


title: B3m_CAM

description:
Library name: S591_52_B3m_MG_S52_R1_001.fastq.gz
no_correction


title: R002, BCRseq

description: Library name: R002-BCR

data_processing:
Raw reads were aligned using standard BD processing pipelines on SevenBridges Genomics cloud computing platform.
Processing output files were combined using custom code which can be found at https://github.com/csbader/Bader-CS-et-al-2025.
Assembly: GRCh38
Supplementary files format and content: all_sample_rna is a Seurat object .rds with all sample counts and associated metadata.
Supplementary files format and content: all_samples_vdj is an .rds dataframe with all sample VDJ information and matching barcodes to all_sample_rna.

extract_protocol:
Cells were captured and lysed using the BD Rhapsody platform.
Targeted Human Immune Response Panel and VDJ libraries were generated according to manufactuer instructions.

treatment_protocol: Patients either received Orca-T immunotherapy or PBSC grafts ~3 weeks before PBMC isolation, sorting, and capture.

value: Sorted lymphocytes


title: EO771-CSCs,replicate 2

description: Library name: Sample5


title: B3m_MG

description:
Library name: S591_51_B3m_CAM_S51_R1_001.fastq.gz
no_correction


title: B2m_CAM

description:
Library name: S591_50_B2m_MG_S50_R1_001.fastq.gz
no_correction


title: B2m_MG

description:
Library name: S591_49_B2m_CAM_S49_R1_001.fastq.gz
no_correction


title: PBMC, PBSC, rep1

description: Library name: R018


title: PBMC, OrcaT, rep1

description: Library name: R016


title: V4f_CAM

description:
Library name: S591_48_V4f_MG_S48_R1_001.fastq.gz
no_correction

value: Vehicle+LPS


title: V2m_CAM

description:
Library name: S591_46_V2m_MG_S46_R1_001.fastq.gz
no_correction


title: EO771-CSCs,replicate 1

description: Library name: Sample4


title: PBMC, PBSC, rep2

description: Library name: R026


title: EO771-non-CSCs,replicate 2

description: Library name: Sample2


title: V2m_MG

description:
Library name: S591_45_V2m_CAM_S45_R1_001.fastq.gz
no_correction


title: V4f_MG

description:
Library name: S591_47_V4f_CAM_S47_R1_001.fastq.gz
no_correction


title: Stationary reference culture, with 50 mM metformin, replicate 3

city: Irapuato

first: Jimena

middle: Meneses

last: Plascencia

state: Guanajuato

address: Libramiento Norte Km 9.6, 36821 Irapuato, Gto.

department: UGA-LANGEBIO

country: Mexico

institute: CINVESTAV

description:
Library name: Sample 14
Em5_counts

data_processing:
Low-quality bases and adapter sequences were trimmed using FASTP
Trimmed reads were aligned to the reference genome using STAR and filtered by mapping quality with Samtools
Read counts were obtained using HTSeq
Data normalization was performed with the RUVseq package
Assembly: GCF_000146045.2
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Saccharomyces cerevisiae

source_name: haploid yeast

growth_protocol: Pre-inoculums of the WT strain were established by culturing individual colonies in 10 mL of SC medium (pH 4) at 30 °C with shaking (200 rpm) for 24 h. Cultures were then diluted to an OD₆₀₀ of 0.05 in 50 mL of SC medium (pH 4), with or without metformin, and incubated under the same conditions.

extract_protocol:
Total RNA was extracted using the RiboPure™ Yeast Kit (Invitrogen AM1926).
Directional-Ribodepletion

treatment_protocol: Cell were treated with 50 mm of metformin (Sigma D150959) or without metformin.

value: haploid yeast

value: MATa his3D::kanMX4 PDC1-RFP-CaURA3MX4 can1D::STE2pr-SpHIS5 lyp1D LEU2 his3D1 ura3D0

tag: phase

value: Stationary phase

value: 50 mM metformin


title: EO771-non-CSCs,replicate 1

description: Library name: Sample1


title: V1m_CAM

description:
Library name: S591_44_V1m_MG_S44_R1_001.fastq.gz
no_correction

value: Brain devoid of choroid plexuses


title: DSP-1001660015357-A-G08_AHFYT3DSX5

city: Boston

first: Fangyuan

last: Chen

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Library name: DSP-1001660015357-A-G08_AHFYT3DSX5

data_processing:
The raw data were quantile normalized for epithelial sections (ER-Hi, ER-Lo, ER-Neg) and stromal segments (Stroma) separately.
Assembly: hg38
Supplementary files format and content: Data is distributed as raw files (DCC), pkc file provided
Library strategy: Spatial Transcriptomics

source_name: breast cancer

extract_protocol: Following NanoString Digital Spatial Profiler protocol ((v1.0) Human NGS Whole Transcriptome Atlas)

value: breast cancer

tag: sample group

value: ER-Neg


title: DSP-1001660015357-A-G09_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G09_AHFYT3DSX5

value: Stroma


title: EO771-non-CSCs,replicate 3

description: Library name: Sample3


title: DSP-1001660015357-A-G06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G06_AHFYT3DSX5

value: ER-Hi


title: Stationary reference culture, with 50 mM metformin, replicate 2

description:
Library name: Sample 13
Em2_counts


title: Stationary reference culture, with 50 mM metformin, replicate 1

description:
Library name: Sample 12
Em1_counts


title: 5f_MG

description:
Library name: S591_42_5f_MG_S42_R1_001.fastq.gz
no_correction

value: untreated+PBS


title: RNA-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 2

city: Wako

first: Nayan

last: Suryawanshi

state: Saitama

address: Hirosawa 2-1

department: Center for Brain Science

country: Japan

institute: RIKEN

description:
Library name: cLTP2.RNA
cLTP2-RNA-seq

data_processing:
For Ribo-seq, adapters were trimmed using cutadapt -a CTGTAGGCACCATCAAT -u 1 -m 11, aligned to rRNA using Bowtie, aligned to mouse transcriptome and genome using Bowtie and STAR, respectively. And furhter processed with samtools and bedtools.
For RNA-seq, samples were demultiplexed and adpater were trimmed using cutadapt -u 8 -m 11, aligned to rRNA using Bowtie, aligned to mouse transcriptome and genome using Bowtie and STAR, respectively. And furhter processed with samtools and bedtools.
Assembly: mm39 and nucleotide sequences of all transcripts on the reference chromosomes
Supplementary files format and content: A tab-delimited text file contains raw counts for all predicted ORFs with columns for transcript id (V1), chromosome(V2), strand (V3), number of ORFs (V4), trnascript length (V5), ORF START (V6), ORF STOP (V7), ORF type (V8), START codon preference (V9) , and Ribo-seq raw counts from each samples: TTX1, TTX2, TTX3, cLTP1, cLTP2, and cLTP3
Supplementary files format and content: A tab-delimited text file include columns for transcript id (V1), RNA-seq and Ribo-seq raw counts from each samples: TTX1.Ribo, TTX2.Ribo, TTX3.Ribo, cLTP1.Ribo, cLTP2.Ribo, cLTP3.Ribo, TTX1.RNA, TTX2.RNA, TTX3.RNA, cLTP1.RNA, cLTP2.RNA, and cLTP3.RNA

source_name: Hippocampus

growth_protocol: Organotypic hippocampal slice cultures were prepared as described previously by Stoppini et al 49. In brief, hippocampal slices of 325 μm thickness were dissected from both male and female C57BL/6N mice (SLC) at the postnatal day 5-6 (P5-6) using a McIlwain tissue chopper (The Mickle Laboratory Engineering), and were plated on hydrophilic PTFE membranes (Millicell, Millipore). The slices were maintained in a culture medium containing MEM (Sigma-Aldrich), 20% heat-inactivated horse serum (GIBCO), 1 mM glutamax (GIBCO), 1 mM CaCl2, 2 mM MgSO4, 12.9 mM D-Glucose, 5.2 mM NaHCO3, 30 mM HEPES, 0.075% ascorbic acid, 1 µg/ml insulin at 37℃ in a 5% CO2 humidified at-mosphere. The culture medium was exchanged with fresh medium every other day.

extract_protocol:
RNA extraction was performed as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012)
For Ribo-seq, Library construction was performed as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012). For RNA-seq, RNA was used to purify mRNA using Takara Oligotex-dT30 kit according to manufac-turer’s instructions. Purified RNA was fragmented using alkaline fragmentation buffer containing 27 mM Na2CO3 , 72 mM NaHCO3 , 2 mM EDTA, at 95 ℃ for 40 min. Fragments corresponding the length of 25 to 34 nt were used for the library construction using protocol describe above.

treatment_protocol: At day in vitro 2 (DIV2), cultured slices were divided into the two groups and AAV vectors at a titer of 0.5 x 1013 GC were directly added onto cultures, as follows: AAV-DJ-hSyn1-EGFP-L10a and AAV-DJ-hSyn1-HA-GFP-nanobody-HALO-PEST for control group and AAV-DJ-hSyn1-EGFP-L10a and AAV-DJ-ESARE-HA-GFP-nanobody-HALO-PEST for stimulation group. At DIV15-16, the culture medium was replaced by media containing 1 µM TTX (Tocris and Wako). At DIV16-17, slices were either treated with cLTP cocktail or 1 µM TTX for 15 min. cLTP cocktail containing 50 µM forskolin (Abcam), 0.1 µM rolipram (Sigma), 50 µM (+)-bicuculline (Tocris), and 100 µM 4-aminopyridine (Tocris) was prepared in artificial cerebrospinal fluid (ACSF) composed of 15 mM Hepes pH 7.3, 125 mM NaCl, 20 mM Glucose, 5 mM KCl, and 4 mM CaCl2. After the stimulation, the slices were al-lowed to recover for 1 h in normal culture media. Slices were then briefly washed with ice-cold PBS, immediately frozen in liquid nitrogen and stored at -80℃ until processed for Ribo-seq and RNA-seq.

value: Hippocampus

value: cLTP


title: V1m_MG

description:
Library name: S591_43_V1m_CAM_S43_R1_001.fastq.gz
no_correction

value: CAMs


title: 5f_CAM

description:
Library name: S591_41_5f_CAM_S41_R1_001.fastq.gz
no_correction

value: Ccr2 KO


title: Stationary reference culture, without metformin, replicate 2

description:
Library name: Sample 10
Ec2_counts

value: 0 mM metformin


title: Stationary reference culture, without metformin, replicate 3

description:
Library name: Sample 11
Ec5_counts


title: 3m_MG

description:
Library name: S591_40_3m_MG_S40_R1_001.fastq.gz
no_correction

value: Microglia


title: DSP-1001660015357-A-G04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G04_AHFYT3DSX5


title: DSP-1001660015357-A-G05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G05_AHFYT3DSX5


title: RNA-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 1

description:
Library name: cLTP1.RNA
cLTP1-RNA-seq


title: RNA-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 3

description:
Library name: cLTP3.RNA
cLTP3-RNA-seq


title: Stationary reference culture, without metformin, replicate 1

description:
Library name: Sample 9
Ec1_counts


title: DSP-1001660015357-A-G03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G03_AHFYT3DSX5

value: ER-Lo


title: RNA-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 3

description:
Library name: TTX3.RNA
TTX3-RNA-seq

value: TTX


title: Exponential culture, with 50 mM metformin, replicate 4

description:
Library name: Sample 8
Mm4_counts

value: haploid yeast

value: MATa his3D::kanMX4 PDC1-RFP-CaURA3MX4 can1D::STE2pr-SpHIS5 lyp1D LEU2 his3D1 ura3D0

value: Exponential phase


title: 3m_CAM

description:
Library name: S591_39_3m_CAM_S39_R1_001.fastq.gz
no_correction

value: Brain devoid of choroid plexuses


title: DSP-1001660015357-A-G01_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G01_AHFYT3DSX5

value: breast cancer


title: DSP-1001660015357-A-G07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G07_AHFYT3DSX5


title: RNA-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 1

description:
Library name: TTX1.RNA
TTX1-RNA-seq


title: RNA-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 2

description:
Library name: TTX2.RNA
TTX2-RNA-seq


title: Exponential culture, with 50 mM metformin, replicate 2

description:
Library name: Sample 6
Mm2_counts

value: 50 mM metformin


title: 1m_CAM

description:
Library name: S591_37_1m_CAM_S37_R1_001.fastq.gz
no_correction


title: DSP-1001660015357-A-F12_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F12_AHFYT3DSX5

value: ER-Neg


title: DSP-1001660015357-A-F11_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F11_AHFYT3DSX5


title: Exponential culture, with 50 mM metformin, replicate 1

description:
Library name: Sample 5
Mm1_counts


title: 14_MG

description:
Library name: S591_16_14_MG_S16_R1_001.fastq.gz
no_correction

value: Wild type


title: Exponential culture, without metformin, replicate 4

description:
Library name: Sample 4
Mc4_counts


title: 1m_MG

description:
Library name: S591_38_1m_MG_S38_R1_001.fastq.gz
no_correction

value: untreated+PBS


title: 14_CAM

description:
Library name: S591_15_14_CAM_S15_R1_001.fastq.gz
IEG_correction


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 3

description:
Library name: cLTP3.Ribo
cLTP3-Ribo-seq

library_source: other

molecule: other

value: Hippocampus


title: Exponential culture, without metformin, replicate 3

description:
Library name: Sample 3
Mc3_counts


title: DSP-1001660015357-A-F10_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F10_AHFYT3DSX5

value: ER-Hi


title: DSP-1001660015357-A-F09_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F09_AHFYT3DSX5

value: Stroma


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 3

description:
Library name: TTX3.Ribo
TTX3-Ribo-seq


title: DSP-1001660015357-A-G02_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-G02_AHFYT3DSX5


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 2

description:
Library name: cLTP2.Ribo
cLTP2-Ribo-seq

value: cLTP


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 2

description:
Library name: TTX2.Ribo
TTX2-Ribo-seq


title: Exponential culture, with 50 mM metformin, replicate 3

description:
Library name: Sample 7
Mm3_counts


title: 15_CAM

description:
Library name: S591_17_15_CAM_S17_R1_001.fastq.gz
no_correction

value: CAMs


title: DSP-1001660015357-A-F08_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F08_AHFYT3DSX5


title: 15_MG

description:
Library name: S591_18_15_MG_S18_R1_001.fastq.gz
no_correction

value: Microglia


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 1

description:
Library name: cLTP1.Ribo
cLTP1-Ribo-seq


title: 12_MG

description:
Library name: S591_14_12_MG_S14_R1_001.fastq.gz
no_correction


title: Exponential culture, without metformin, replicate 2

description:
Library name: Sample 2
Mc2_counts

value: 0 mM metformin


title: 12_CAM

description:
Library name: S591_13_12_CAM_S13_R1_001.fastq.gz
IEG_correction


title: DSP-1001660015357-A-F07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F07_AHFYT3DSX5

value: ER-Lo


title: DSP-1001660015357-A-F06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F06_AHFYT3DSX5


title: syN-CAR-exo

city: Changchun

first: Jiayi

last: chen

state: 吉林Jilin

address: School of Life Sciences

institute: Jilin University

description:
Library name: sample 2
10x Genomics

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, celltanger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically.
Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by marker gene.
KEGG (Kanehisa M, 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
10x Genomics® Cell Preparation Guide describes best practices and general protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina).

value: lung

value: syN-CAR-exo


title: DSP-1001660015357-A-F05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F05_AHFYT3DSX5


title: Staphylococcus aureus_Corynebacterium striatum, co_culture2

city: 广州

first: Zhou

last: Jiewen

address: 广东省广州市越秀区中山大学北校区

institute: 中山大学附属第一医院

description: Library name: SA_CS2

data_processing:
The RNA-sequencing data were processed through a series of quality control steps using FastQC (version 0.11.9).
Fastp (version 0.39) was employed to filter out low-quality reads and adapter sequences.
The clean reads were then aligned to the human reference genome (hg38) using the HISAT2 alignment tool (version 2.2.1).
Assembly: StringTie assembler (version 2.1.4)
Supplementary files format and content: tab-delimited text file includes raw counts

organism:
Staphylococcus aureus
Corynebacterium striatum

extract_protocol:
RNA extraction from samples was accomplished using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA), following the manufacturer’s prescribed protocol.
RNA-sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA), following the recommended kit procedures.

value: bacteria

value: WT


title: 11_CAM

description:
Library name: S591_11_11_CAM_S11_R1_001.fastq.gz
no_correction

value: Brain devoid of choroid plexuses


title: Staphylococcus aureus_Corynebacterium striatum, co_culture3

address: 广东省广州市越秀区中山大学北校区

description: Library name: SA_CS3


title: PBS

description:
Library name: sample 1
10x Genomics

value: PBS


title: Liver, Upstream, Greenside Darters, biol rep 6

city: Waterloo

first: Louis

middle: Joseph

last: Pfeifer

state: ON

address: 200 University Ave W

department: Biology

country: Canada

institute: University of Waterloo

description:
Library name: GK7_S30
Column name in G_Trinity_trans_gene_counts_matrix.txt: GK7_S30

data_processing:
Raw paired-end reads were processed using Trimmomatic (v0.36) (Sliding Window: 5:20; leading/trailing threshold: 20) to remove sequences with low-quality bases (Q<20), trim adapters and low quality leading/trailing ends, and filter sequences shorter than 45 bp
Trimmed reads were assembled de novo with Trinity (v2.13.2) under default parameters
Reads were mapped to their respective assemblies using Bowtie2 (v2.2.7) and abundance estimation using RSEM (v1.3.1)
Assembly: Trimmed reads were assembled de novo with Trinity (v2.13.2) under default parameters
Supplementary files format and content: Tab-delimited text file including raw counts for each sample
Supplementary files format and content: Tab-delimited text file including TPM values for each sample

organism: Etheostoma blennioides

source_name: Liver

extract_protocol:
RNA was extracted using QIAzol and chloroform (Qiagen), precipitated with isopropanol, eluted with 50μl of nuclease free water. 2 ug of totla RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols

value: Liver

value: Upstream


title: Staphylococcus aureus_Corynebacterium striatum, co_culture1

address: 广东省广州市越秀区中山大学北校区

description: Library name: SA_CS1


title: 9_MG

description:
Library name: S591_10_9_MG_S10_R1_001.fastq.gz
no_correction

value: Wild type

value: untreated+PBS


title: 9_CAM

description:
Library name: S591_09_9_CAM_S9_R1_001.fastq.gz
IEG_correction


title: 11_MG

description:
Library name: S591_12_11_MG_S12_R1_001.fastq.gz
no_correction


title: Liver, Upstream, Greenside Darters, biol rep 5

description:
Library name: GK6_S29
Column name in G_Trinity_trans_gene_counts_matrix.txt: GK6_S29


title: DSP-1001660015357-A-F03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F03_AHFYT3DSX5

value: breast cancer


title: DSP-1001660015357-A-F02_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F02_AHFYT3DSX5

value: ER-Hi


title: Ribo-seq, Postnatal day 5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 1

description:
Library name: TTX1.Ribo
TTX1-Ribo-seq

value: Hippocampus

value: TTX


title: M2_P_exo_1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
GO enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.  We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: GRCm38/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 and raw counts values for each Sample

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.
In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: macrophage

tag: time

value: Day 2


title: Liver, Upstream, Greenside Darters, biol rep 4

description:
Library name: GK5_S28
Column name in G_Trinity_trans_gene_counts_matrix.txt: GK5_S28


title: M2_P_exo_2

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples


title: M2_3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples


title: DSP-1001660015357-A-F04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F04_AHFYT3DSX5

value: ER-Neg


title: DSP-1001660015357-A-F01_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-F01_AHFYT3DSX5

value: Stroma


title: M2_P_exo_3

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples

value: syN-CAR-exo


title: Exponential culture, without metformin, replicate 1

description:
Library name: Sample 1
Mc1_counts

value: haploid yeast

value: MATa his3D::kanMX4 PDC1-RFP-CaURA3MX4 can1D::STE2pr-SpHIS5 lyp1D LEU2 his3D1 ura3D0

value: Exponential phase

value: 0 mM metformin


title: 8_MG

description:
Library name: S591_08_8_MG_S8_R1_001.fastq.gz
no_correction

value: Brain devoid of choroid plexuses

value: Microglia


title: M2_2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples

value: WT


title: Liver, Upstream, Greenside Darters, biol rep 3

description:
Library name: GK4_S27
Column name in G_Trinity_trans_gene_counts_matrix.txt: GK4_S27

value: Liver

value: Upstream


title: 6_MG

description:
Library name: S591_06_6_MG_S6_R1_001.fastq.gz
no_correction

value: Wild type

value: Vehicle+LPS


title: DSP-1001660015357-A-E12_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E12_AHFYT3DSX5

value: breast cancer


title: M2_1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples

value: macrophage


title: 6_CAM

description:
Library name: S591_05_6_CAM_S5_R1_001.fastq.gz
IEG_correction

value: CAMs


title: Liver, Upstream, Greenside Darters, biol rep 1

description:
Library name: GK2_S25
Column name in G_Trinity_trans_gene_counts_matrix.txt: GK2_S25


title: 4_MG

description:
Library name: S591_04_4_MG_S4_R1_001.fastq.gz
no_correction


title: Liver, Downstream, Greenside Darters, biol rep 6

description:
Library name: GE6_S24
Column name in G_Trinity_trans_gene_counts_matrix.txt: GE6_S24

value: Downstream


title: DSP-1001660015357-A-E10_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E10_AHFYT3DSX5

value: ER-Hi


title: M1_3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples

value: LPS, 100ng/mL

value: Day 2


title: M1_1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples


title: M1_2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt:  raw_counts_All_Samples


title: 4_CAM

description:
Library name: S591_03_4_CAM_S3_R1_001.fastq.gz
IEG_correction


title: Liver, Downstream, Greenside Darters, biol rep 5

description:
Library name: GE5_S23
Column name in G_Trinity_trans_gene_counts_matrix.txt: GE5_S23


title: DSP-1001660015357-A-E08_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E08_AHFYT3DSX5

value: ER-Neg


title: 1_MG

description:
Library name: S591_02_1_MG_S2_R1_001.fastq.gz
no_correction


title: Liver, Downstream, Greenside Darters, biol rep 4

description:
Library name: GE4_S22
Column name in G_Trinity_trans_gene_counts_matrix.txt: GE4_S22


title: 8_CAM

description:
Library name: S591_07_8_CAM_S7_R1_001.fastq.gz
no_correction


title: Liver, Upstream, Greenside Darters, biol rep 2

description:
Library name: GK3_S26
Column name in G_Trinity_trans_gene_counts_matrix.txt: GK3_S26


title: 1_CAM

description:
Library name: S591_01_1_CAM_S1_R1_001.fastq.gz
IEG_correction


title: Liver, Downstream, Greenside Darters, biol rep 3

description:
Library name: GE3_S21
Column name in G_Trinity_trans_gene_counts_matrix.txt: GE3_S21


title: DSP-1001660015357-A-E07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E07_AHFYT3DSX5

value: ER-Lo


title: islets of PBKO mice1

description: Library name: K1

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Assembly: Mus_musculus_ensembl_99
Supplementary files format and content: matrix files

extract_protocol:
The islets of Brd4 conditional knockout (PBKO) and control mice were isolated using  type XI collagenase and were dissociated using a trypsin EDTA solution for sequencing experiments.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

value: islets


title: DSP-1001660015357-A-E11_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E11_AHFYT3DSX5


title: D1_contra_tissue

description:
Library name: S593_32_D1_C_S16_R1_001.fastq.gz
-

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17 software, which resulted in .bcl files, which were converted into fastq files with the bcl2fastq v2.20 software.
Bulk RNA-seq data was aligned with STAR v2.7.11a to the mouse reference genome Gencode M36. Counts were obtained using FeatureCounts v2.0.8. Data was analyzed using DESeq2 1.46.0.
Assembly: Gencode M36
Supplementary files format and content: Processed counts are provided in the files Stroke_CAMs_counts_GEO.txt and Stroke_Milieu_counts_GEO.txt

source_name: Brain

extract_protocol:
Cells were sorted with a MACS Quant Tyto from Miltenyi into RNAprotect Cell Reagent (QIAGEN) according to the manufacturers recommendations. Two samples showed degraded RNA, likely because of too low RNA cell protect reagent vs sorting buffer ratio in the tube. Total RNA was extracted from FACS sorted cells stabilized in RNAprotect Cell Reagent according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamination was removed by using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added, and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation with Illumina Nextera XT Sample Preparation. The sequencing run was performed on a HiSeq 1000 instrument (Control Software v2.2.68) using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

treatment_protocol: WT mice were either treated with Vehicle solution or with 200 mg/KG BW BLZ945. Eight weeks after treatment, mice were subjected to a thromboembolic MCAo model of ischemic stroke.

value: Brain

value: whole brain tissue


title: DSP-1001660015357-A-E05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E05_AHFYT3DSX5

value: Stroma


title: Liver, Downstream, Greenside Darters, biol rep 2

description:
Library name: GE2_S20
Column name in G_Trinity_trans_gene_counts_matrix.txt: GE2_S20

value: Liver


title: islets of control mice2

description: Library name: C2


title: DSP-1001660015357-A-E09_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E09_AHFYT3DSX5


title: DSP-1001660015357-A-E06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E06_AHFYT3DSX5


title: islets of PBKO mice2

description: Library name: K2


title: D1_ipsi_tissue

description:
Library name: S593_31_D1_I_S15_R1_001.fastq.gz
-


title: Liver, Downstream, Greenside Darters, biol rep 1

description:
Library name: GE1_S19
Column name in G_Trinity_trans_gene_counts_matrix.txt: GE1_S19


title: C4_contra_tissue

description:
Library name: S593_30_C4_C_S14_R1_001.fastq.gz
-


title: DSP-1001660015357-A-E04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E04_AHFYT3DSX5


title: SM,susceptible,Xoo,rep3

city: Hyderabad

first: Ramesh

middle: Venkata

last: Sonti

state: Telangana

address: Habsiguda

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

description:
Library name: SM_Xoo_3
S24-3_S366
sm_gene_counts.txt

data_processing:
The raw data was obtained, and the quality was assessed using FastQC.
Adapters and low-quality reads were trimmed using Trim Galore!
RNA-STAR was used to align the trimmed reads to the rice genome (MSU Rice Genome Annotation Project - version 7)
Reads that mapped to the genes were quantified using featureCounts
Differential gene expression was obtained using the R library DEseq2
Assembly: MSU Rice Genome Annotation Project - version 7
Supplementary files format and content: Format: txt; Description: Raw gene counts as obtained using FeatureCounts
Supplementary files format and content: Format: txt; Description: Normalised gene expression values obtained using DEseq2

organism: Oryza sativa

source_name: Leaf

growth_protocol: Plants were grown till maximum tillering stage in natural field conditions, transferred to green house one-week prior to the inoculation and grown at 30 degree celcius

extract_protocol:
Total RNA was extraced using Qiagen Rneasy plant DNA isolation kit by following recommended protocols.
Purified RNA was quantified using QubitTM RNA HS Assay Kit (Thermo Fisher Scientific, USA). RNA integrity was assessed using agarose gel electrophoresis and BioAnalyzer 2100 (Agilent Technologies, USA). 1 µg of intact total RNA samples were used for library preparation using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, USA). Sequencing was performed on Illumina’s NovaSeq6000 platform with cycling conditions to obtain 2x100bp reads on an S2 flow cell.

treatment_protocol: The leaves were treated with Xoo strain IXO1221 that was set at OD 1 by clip inoculation. Samples were collected as 1cm long leaf pieces from the site of clipping immediately post inoculation (o hpi or mock) or at 24 hpi.

value: Leaf

value: SM

value: Xoo


title: DSP-1001660015357-A-E03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E03_AHFYT3DSX5

value: breast cancer


title: SM,susceptible,Xoo,rep1

description:
Library name: SM_Xoo_1
S24-1_S364
sm_gene_counts.txt


title: islets of control mice1

description: Library name: C1


title: C3_contra_tissue

description:
Library name: S593_28_C3_C_S12_R1_001.fastq.gz
-

value: Wild type


title: sample 2 of liver sinusoidal endothelial cells exposed to hydrostatic pressure stimulation

city: Suita

first: Seiya

last: Kato

state: Osaka

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

institute: Osaka University

description: Library name: HP2

data_processing:
The sequenced reads were mapped to a mouse reference genome sequence (mm10) using TopHat ver. 2.2.1. The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-separated values files containing raw counts

source_name: liver

extract_protocol:
After a cell suspension was generated, hepatocytes were eliminated via low-speed centrifugation (50xg), and dead cells and erythrocytes were eliminated via density gradient centrifugation using Percoll PLUS (GE17-5445-02; Cytiva). LSECs were selected using MACS CD146 MicroBeads (132-092-007; Miltenyi Biotec). Primary murine LSECs were exposed to hydrostatic pressure (HP) stimulation. After incubation on a Collagen I-coated plate overnight, the cells were serum-starved for 6 hours and then exposed to periodic HP stimulation for repeated cycles (0.01 Hz) between 101 and 135 kPa (absolute) for 8 hours using our original HPS system. The system was maintained at 37°C in a CO2 incubator (5% CO2).
Library preparation was carried out using a TruSeq stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s instructions. Whole-transcriptome sequencing was performed on an Illumina NovaSeq 6000 sequencer in 101-base single-read mode.

value: liver

value: endothelial cells

value: wild


title: sample 3 of liver sinusoidal endothelial cells exposed to hydrostatic pressure stimulation

description: Library name: HP3

treatment_protocol: Primary murine LSECs were exposed to hydrostatic pressure (HP) stimulation.


title: Lung, wildtype and knock out, bleomycin injury

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

description:
Library name: sublibrary1 and sublibrary2
wildtype and knock out are in the same sequencing library

data_processing:
ParseBiosceinces-Pipeline 1.1.2 was used with default setting for demultiplexing, aligning reads to mouse GRCm39 reference genome.
Assembly: GRCm39
Supplementary files format and content: for each sample, the DGE_filtered folder files

extract_protocol:
The young control and bleomycin-injured WT and Sdc1–/– cohort details was published (18). For the aged mouse cohort, freshly harvested bleomycin-injured WT and Sdc1–/–mouse lungs were enzymatically digested with elastase (Worthington Biochemical Corporation, Lakewood, NJ) and liberase (RocheTM, Millipore-Sigma) and mechanically disrupted to generate single cell suspension per previously published protocol (43). Viable lung cell suspension (DAPI¯) was flow-sorted for lung immune cells (CD45+), endothelial cells (CD31+), epithelial cells (CD326+), and stromal cells (CD45¯CD31¯CD326¯).
Equal proportions of all four cell types were pooled and subjected to single-cell capture using EvercodeTM WT mini kit v2 for barcoding and library preparation (Parse Bioscience, Seattle, WA) following the manufacturer’s protocol.
Novaseq SP at 200 cycles, 800 million reads

value: lung

value: mixed sample (wildtype and knock out )

value: bleomycin injury


title: C2_contra_tissue

description:
Library name: S593_26_C2_C_S10_R1_001.fastq.gz
-


title: DSP-1001660015357-A-E02_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E02_AHFYT3DSX5

value: ER-Hi


title: SM,susceptible,mock,rep2

description:
Library name: SM_Mock_2
S0-2_S362
sm_gene_counts.txt

value: Mock


title: DSP-1001660015357-A-E01_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-E01_AHFYT3DSX5


title: C3_ipsi_tissue

description:
Library name: S593_27_C3_I_S11_R1_001.fastq.gz
-

value: Brain


title: DSP-1001660015357-A-D12_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D12_AHFYT3DSX5

value: ER-Neg


title: sample 3 of liver sinusoidal endothelial cells as a control

description: Library name: control3


title: SM,susceptible,mock,rep3

description:
Library name: SM_Mock_3
S0-3_S363
sm_gene_counts.txt


title: sample 1 of liver sinusoidal endothelial cells exposed to hydrostatic pressure stimulation

description: Library name: HP1


title: C4_ipsi_tissue

description:
Library name: S593_29_C4_I_S13_R1_001.fastq.gz
-

value: whole brain tissue


title: DSP-1001660015357-A-D11_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D11_AHFYT3DSX5

value: ER-Lo


title: SM,susceptible,mock,rep1

description:
Library name: SM_Mock_1
S0-1_S361
sm_gene_counts.txt

value: Leaf


title: C2_ipsi_tissue

description:
Library name: S593_25_C2_I_S9_R1_001.fastq.gz
-


title: sample 2 of liver sinusoidal endothelial cells as a control

description: Library name: control2


title: B1_contra_tissue

description:
Library name: S593_24_B1_C_S8_R1_001.fastq.gz
-

value: Veh


title: DSP-1001660015357-A-D10_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D10_AHFYT3DSX5


title: SM,susceptible,Xoo,rep2

description:
Library name: SM_Xoo_2
S24-2_S365
sm_gene_counts.txt

value: SM

value: Xoo


title: sample 1 of liver sinusoidal endothelial cells as a control

description: Library name: control1


title: B1_ipsi_tissue

description:
Library name: S593_23_B1_I_S7_R1_001.fastq.gz
-

value: Wild type


title: WT mouse 14 days post infected

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description: Library name: D14-5_230621N_S115_L003

data_processing:
The original sequencing data were analyzed by using FastQC software. 10X Chromium single cell transcriptome sequencing can be divided into three regions near the polyA and five regions near the transcriptional initiation site. Among them, 5-terminal transcript sequencing is usually performed together with T cell and B cell receptor gene TCR/BCR sequences for sequencing analysis. Different kits (including 3-terminal vs 5-terminal, and different versions) have slightly different library structures: For example, for a sample processed by a 10X single-cell 3-terminal V2 kit, Read 1 consists of a 16bp 10X Cell Barcode and a 10bp UMI sequence; The sample processed by the V3 kit, Read 1, consisted of 16 bp 10X Cell Barcode and 12 bp UMI sequence. In the analysis, 10X Cell Barcode in Read1 was used to separate individual cells, and UMI was used to remove PCR amplification bias and distinguish between transcripts. Read2 is a 151 bp cDNA sequence, and the first 91 bp is generally used for downstream analysis of Cell Ranger.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.26_GRCm38.p6.v2201
Supplementary files format and content: Matrix table wuth raw gene counts for every gene and every cell

extract_protocol:
For the inspection and counting of single-cell suspension, the survival rate of cells is generally required to be above 85%, and the qualified cells are prepared by washing and re-suspension into a suitable cell concentration of 700~1200 cells/µl
According to the expected number of target cells, Gel Bead in Emulsion was constructed for single cell separation. After the normal formation of GEMs, GEMs were collected for reverse transcription in PCR instrument to realize labeling. For GEMs oil breaking treatment, a strand of cDNA was purified and enriched with magnetic beads, then cDNA amplification and quality inspection were carried out. The qualified cDNA was constructed by the second generation sequencing library, and the quantitative quality of the library was finally tested through the experimental processes of fragmentation, connecting sequencing joints, and sample Index PCR.

value: WT

value: infected

tag: time point

value: 14 days post infected


title: DSP-1001660015357-A-D09_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D09_AHFYT3DSX5

value: breast cancer

value: Stroma


title: A4_contra_tissue

description:
Library name: S593_22_A4_C_S6_R1_001.fastq.gz
-


title: DSP-1001660015357-A-D08_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D08_AHFYT3DSX5


title: BB42,resistant,Xoo,rep2

description:
Library name: BB42_Xoo_2
B24-2-RS_S371
bb42_gene_counts.txt


title: A4_ipsi_tissue

description:
Library name: S593_21_A4_I_S5_R1_001.fastq.gz
-


title: BB42,resistant,mock,rep2

description:
Library name: BB42_Mock_2
B0-2_S368
bb42_gene_counts.txt


title: A2_contra_tissue

description:
Library name: S593_18_A2_C_S2_R1_001.fastq.gz
-


title: BB42,resistant,mock,rep3

description:
Library name: BB42_Mock_3
B0-3_S369
bb42_gene_counts.txt


title: GL261_ZBTB7B

city: DaLian

first: YiDing

last: Liu

address: wwde

institute: Dalian Medical University

description:
Library name: GL261_ZBTB7B
Treated

data_processing:
Remove reads containing adapters
Remove reads containing N (where N represents undetermined base information)
Remove low-quality reads (reads where the number of bases with Qphred ≤ 5 accounts for more than 50% of the total read length)
Assembly: mm10,hg38
Supplementary files format and content: all_compare1.txt,all_compare2.txt
Supplementary files format and content: counts values for each Sample

extract_protocol:
To extract RNA from samples, the Trizol method was used. After successful extraction, the RNA was dissolved in 50 µL of DEPC-treated water. Subsequently, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of  the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: glioma cells

value: overexpression ZBTB7B

value: Treated


title: DSP-1001660015357-A-D06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D06_AHFYT3DSX5

value: ER-Hi


title: WT mouse 7 days post infected

description: Library name: D7-5_230612N_S287_L003

value: lung

value: 7 days post infected


title: BB42,resistant,Xoo,rep3

description:
Library name: BB42_Xoo_3
B24-3-RS_S372
bb42_gene_counts.txt


title: BB42,resistant,mock,rep1

description:
Library name: BB42_Mock_1
B0-1_S367
bb42_gene_counts.txt

value: Mock


title: A3_ipsi_tissue

description:
Library name: S593_19_A3_I_S3_R1_001.fastq.gz
-

value: Brain

value: whole brain tissue


title: Staphylococcus aureus, mono culture3

address: 广东省广州市越秀区中山大学北校区

description: Library name: SA3

organism: Staphylococcus aureus

source_name: Staphylococcus aureus, mono culture

value: bacteria


title: A2_ipsi_tissue

description:
Library name: S593_17_A2_I_S1_R1_001.fastq.gz
-

value: Veh


title: A3_contra_tissue

description:
Library name: S593_20_A3_C_S4_R1_001.fastq.gz
-

value: Wild type


title: BB42,resistant,Xoo,rep1

description:
Library name: BB42_Xoo_1
B24-1-RS_S370
bb42_gene_counts.txt

value: Leaf

value: Xoo


title: DSP-1001660015357-A-D07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D07_AHFYT3DSX5

value: ER-Lo


title: DSP-1001660015357-A-D03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D03_AHFYT3DSX5

value: breast cancer


title: DSP-1001660015357-A-D05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D05_AHFYT3DSX5

value: Stroma


title: WT mouse

description: Library name: WT-5_230612N_S288_L003

value: WT

value: uninfected


title: Staphylococcus aureus, mono culture2

address: 广东省广州市越秀区中山大学北校区

description: Library name: SA2


title: naive B WT

city: Beijing

first: xiaocui

last: luo

address: Haidian District

institute: Tsinghua university

description: Library name: mb1-naive

library_source: genomic

data_processing:
ATAC-seq reads were trimmed from 3'end until the final base had a quality score >20, using cutadapt (version=3.5), discarding reads left with <20 bp
Trimmed reads were mapped to the mouse genome (mm10) through bowtie2 (version=2.4.5) with parameter:--very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 \\ -I 10 -X 700 --threads 16.
Duplicated reads were removed by picard MarkDuplicates (Version:2.26.6)
Peaks were visualized by bamCoverage (version=3.5.1) by parameters:--binSize 50  --normalizeUsing RPKM --extendReads
Assembly: mm10
Assembly: Supplementary files format and content: tab-delimited text file includes normalized CDS counts for each sample
Supplementary files format and content: bigWig

source_name: spleen

extract_protocol:
Nuclei were collected and resuspended into 50 μl tagmentation mix, which contains 10 μl 5×TTBL (Vazyme), 5 μl TTE Mix V50 and 35 μl ddH2O. Samples were incubated at 37 °C for 30 min. After tagmentation, fragmented DNA was isolated by using VAHTS DNA Clean Beads.
ATAC libraries were amplified for 12 PCR cycles using TruePrepTM Index Kit V2 for Illumina (Vazyme #TD202). 0.55×VAHTSTM DNA Clean Beads were used to exclude the High–molecular weight DNA, followed by positive selection with 1×beads. High-quality DNA libraries were sequenced on the Illumina HiSeq2000.

treatment_protocol: 5×104 naïve B cells or GCMP cells were sorted from Cd79acre/+ mice and Cd79acre/+Zbtb18fl/fl mice, respectively. Cells were collected by gentle centrifugation (500x g, 5 minutes) at 4 °C, and then resuspended in lysis buffer (10 mM Tris.Cl, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) and incubated on ice for 10 min.

value: spleen

value: naive B cells


title: ZBTB18KO_GCMP2

description: Library name: TB18-MP2

value: memory B cell precursor in germinal center

value: NP-KLH/LPS/Alum 14dpi


title: naive  B ZBTB18KO

description: Library name: TB18-naive


title: GL261_Vector

description:
Library name: GL261_Vector
Control

value: glioma cells

value: Control


title: DSP-1001660015357-A-D02_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D02_AHFYT3DSX5

value: ER-Hi


title: D1_contra_CAM

description:
Library name: S593_16_D1_contra_S40_R1_001.fastq.gz
-

source_name: Brain devoid of choroid plexus

value: Brain devoid of choroid plexus

value: CAMs


title: DSP-1001660015357-A-D04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D04_AHFYT3DSX5

value: ER-Neg


title: DSP-1001660015357-A-D01_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-D01_AHFYT3DSX5


title: ZBTB18KO_GCMP1

description: Library name: TB18-MP1


title: Staphylococcus aureus, mono culture1

address: 广东省广州市越秀区中山大学北校区

description: Library name: SA1

value: bacteria


title: D1_ipsi_CAM

description:
Library name: S593_15_D1_ipsi_S39_R1_001.fastq.gz
-

value: Wild type


title: DSP-1001660015357-A-C12_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C12_AHFYT3DSX5


title: DSP-1001660015357-A-C11_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C11_AHFYT3DSX5

value: ER-Lo


title: C4_contra_CAM

description:
Library name: S593_14_C4_contra_S38_R1_001.fastq.gz
-


title: WT_GCMP2

description: Library name: mb1-MP3


title: DSP-1001660015357-A-C10_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C10_AHFYT3DSX5

value: breast cancer


title: Lyso_R+_N2a_CQ

city: Hefei

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

description: Library name: sample47

data_processing:
For data processing, raw reads were first processed with fastp to obtain clean reads.
Clean Reads were then aligned to the reference genome (Human: hg19; Mouse: mm10; C. elegans: ce10) with BWA-MEM or Bowtie2. For circRNA prediction, backsplicing junctions (BSJs) were identified using both CIRI2 and Find_circ, and BSJ reads identified by CIRI2 were used to quantify circRNAs. For linear RNA, read counts were generated using BEDTools.
Assembly: hg19(human), mm10(mouse), ce11(C. elegans)

source_name: cell line

extract_protocol:
Total RNA from cells or C. elegans strains was extracted by TRIzol Reagent or TRIzol LS Reagent according to the manufacturer?s procedures.
The concentration of isolated RNAs was verified by Nanodrop, and RNA quality was checked with gel electrophoresis. For ribosomal RNA-depleted (Ribo-) RNA-seq, rRNA in total RNA was depleted with the Illumina Ribo-Zero Gold kit (Illumia) and subjected to library preparation with the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer?s instructions. For Ribo-/RNase R+ RNA-seq, total RNA was rRNA-depleted, RNase R-treated and subjected to library preparation according to the manufacturer?s instructions.

value: CQ


title: C3_ipsi_CAM

description:
Library name: S593_11_C3_ipsi_S35_R1_001.fastq.gz
-


title: WT_GCMP1

description: Library name: mb1-MP2


title: Lyso_R+_N2a_BafA1

description: Library name: sample46

value: WT


title: C4_ipsi_CAM

description:
Library name: S593_13_C4_ipsi_S37_R1_001.fastq.gz
-


title: DSP-1001660015357-A-C09_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C09_AHFYT3DSX5

value: Stroma


title: DSP-1001660015357-A-C07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C07_AHFYT3DSX5


title: C3_contra_CAM

description:
Library name: S593_12_C3_contra_S36_R1_001.fastq.gz
-


title: Non-migratory/PpIX-low

type: RNA

city: Bunkyo-ku

first: Kouichi

last: Tabu

state: Tokyo

address: 1-5-45, Yushima

institute: Institute of Science Tokyo

hyb_protocol: Cy3-labeled cRNA was hybridized to Agilent one-color microarrays (Agilent-072363) according to the manufacturer’s recommended protocol.

scan_protocol: Arrays were scanned using an Agilent microarray scanner and the manufacturer’s default one-color settings.

data_processing: Raw feature extraction output files were generated by Agilent Feature Extraction software. Processed/normalized expression values were obtained by CERI using a standard GeneSpring-based pipeline.

source_name: Patient-derived glioblastoma cell line

label_protocol: Cy3-labeled cRNA was prepared from total RNA using an Agilent one-color labeling workflow according to the manufacturer’s instructions.

growth_protocol: Patient-derived glioblastoma cells were maintained under serum-free neurosphere culture conditions using DMEM/F12-based medium supplemented with appropriate growth factors and supplements, as described in the associated manuscript.

extract_protocol: Total RNA was extracted from each fraction/population according to the protocol described in the associated manuscript.

treatment_protocol: Cells were subjected to Transwell migration-based fractionation without extracellular matrix coating. For PpIX-based subdivision, cells were exposed to 5-aminolevulinic acid (5-ALA) and separated into PpIX-high and PpIX-low populations by fluorescence-based sorting.

value: brain

value: patient-derived GBM line

tag: fraction/population

value: Non-migratory fraction (Transwell, no ECM coating) with low 5-ALA–induced PpIX fluorescence


title: DSP-1001660015357-A-C08_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C08_AHFYT3DSX5


title: C2_ipsi_CAM

city: Freiburg

first: Maximilian

last: Fliegauf

institute: Uniklinikum Freiburg

description:
Library name: S593_09_C2_ipsi_S33_R1_001.fastq.gz
RNA degraded


title: C2_contra_CAM

description:
Library name: S593_10_C2_contra_S34_R1_001.fastq.gz
-


title: Lyso_R+_3T3L1_Mock

description: Library name: sample45


title: DSP-1001660015357-A-C06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C06_AHFYT3DSX5


title: B1_contra_CAM

description:
Library name: S593_08_B1_contra_S32_R1_001.fastq.gz
-

value: Veh


title: Lyso_R+_3T3L1_CQ

description: Library name: sample44


title: DSP-1001660015357-A-C05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C05_AHFYT3DSX5


title: Lyso_R+_N2a_Mock

description: Library name: sample48


title: Lyso_R+_3T3L1_BafA1

description: Library name: sample43


title: B1_ipsi_CAM

description:
Library name: S593_07_B1_ipsi_S31_R1_001.fastq.gz
-


title: Migratory/PpIX-high

value: Migratory fraction (Transwell, no ECM coating) with high 5-ALA–induced PpIX fluorescence


title: S-pattern_rep3

city: Kyoto

first: Masahiro

last: Inoue

address: Shimoadachi-cho 46, Sakyou-ku

institute: Kyoto University, Graduate School of Medicine

hyb_protocol: Following fragmentation, 1.65 μg of cRNA was hybridized to the Agilent expression microarray according to the manufacturer’s protocol.

scan_protocol: The microarrays were scanned using a G4900DA SG12494263 instrument (Agilent).

data_processing: Microarray data export, processing, and analysis were performed using Agilent Feature Extraction v11.0.1.1.

source_name: Patient-derived adenoma organoids

label_protocol: Cy3-labeled cRNA was prepared from 1~5 µg of total RNA using the Quick Amp Labeling Kit (Agilent).

growth_protocol: Five hundred organoids for each patient-derived adenoma line were cultured for 6 days in 7 μL of Matrigel GFR after passaging.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN).

tag: tumor stage

value: adenoma


title: A4_contra_CAM

address: Breisacherstraße 113

description:
Library name: S593_06_A4_contra_S30_R1_001.fastq.gz
-


title: D-pattern_rep2


title: Migratory/PpIX-low

value: Migratory fraction (Transwell, no ECM coating) with low 5-ALA–induced PpIX fluorescence


title: RK_R+_N2a_siRK

description: Library name: sample14


title: D-pattern_rep1


title: Non-migratory/PpIX-high

value: Non-migratory fraction (Transwell, no ECM coating) with high 5-ALA–induced PpIX fluorescence


title: D-pattern_rep3


title: DSP-1001660015357-A-C03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C03_AHFYT3DSX5

data_processing:
The raw data were quantile normalized for epithelial sections (ER-Hi, ER-Lo, ER-Neg) and stromal segments (Stroma) separately.
Assembly: hg38
Supplementary files format and content: Data is distributed as raw files (DCC), pkc file provided
Library strategy: Spatial Transcriptomics

extract_protocol: Following NanoString Digital Spatial Profiler protocol ((v1.0) Human NGS Whole Transcriptome Atlas)


title: S-pattern_rep2


title: RNA-seq, P5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 1

description:
Library name: cLTP1.HALO.RNA
cLTP1-RNA-seq

data_processing:
For pair-end RNA-seq (HALO IP-RNA-seq), adpaters were trimmed using --adapter CTGTCTCTTATACACATCT and --adapter2 CTGTCTCTTATACACATCT. Reads were aligned to rRNA, and mouse genome using the nf-core/rnaseq pipeline (Nextflow), and to the mouse transcriptome using Salmon Quant. The resulting alignments were further processed using samtools and bedtools.
Assembly: mm39 and nucleotide sequences of all transcripts on the reference chromosomes
Supplementary files format and content: A tab-delimited text file contains normalised counts for all predicted mORFs with columns for transcript id (V7), RNA-seq normalised counts from each samples: tTTX1, tTTX2, tTTX3, tcLTP1, tcLTP2, and tcLTP3, where t denotes total-RNA.

extract_protocol:
Halo immunoprecipitated ribosomes/polysome was used for RNA extraction as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012)
The RNA isolated from each sample was used to construct sequencing libraries with the SMART-Seq® mRNA Kit (SMARTer Ultra low input RNA library (PolyA_NexteraXT)), following the manufacturer's protocol. First-strand cDNA synthesis (from total RNA or cells) is primed by the 3’ SMART-Seq CDS Primer II A and uses the SMART-Seq v4 Oligonucleotide for template switching at the 5’ end of the transcript. The first-strand cDNA selectively binds to SPRI beads leaving contaminants in solution which is removed by a magnetic separation. The beads are then directly used for PCR amplification. The Advantage 2 Polymerase Mix has been specially formulated for efficient and accurate amplification of cDNA templates by long-distance PCR. PCR-amplified cDNA is purified by immobilization on AMPure XP beads. The beads are then washed with 80% ethanol and cDNA is eluted with Elution Buffer. The sequencing libraries were prepared according to the manufacturer’s instructions of Nextera XT DNA Library Preparation Kit (Illumina). Briefly, 1ng of cDNA go through tagmentation to fragment and tag the DNA with adapter in a single step. Following tagmentation, indexes were attached with PCR using Nextera indexed primer. The final purified product is quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantification kits for Illumina Sequencing platforms) and qualified using the TapeStation HS D5000 ScreenTape (Agilent Technologies). And then the paired-end (2×150 bp) sequencing was performed by the Macrogen using the NovaSeqX platform (Illumina, San Diego, USA).

value: Hippocampus

value: cLTP


title: RK_R+_N2a_siNC

description: Library name: sample13


title: RK_R+_3T3L1_siNC

description: Library name: sample11


title: A4_ipsi_CAM

description:
Library name: S593_05_A4_ipsi_S29_R1_001.fastq.gz
-

value: Brain devoid of choroid plexus

value: CAMs


title: A3_contra_CAM

description:
Library name: S593_04_A3_contra_S28_R1_001.fastq.gz
-

value: Wild type


title: A3_ipsi_CAM

description:
Library name: S593_03_A3_ipsi_S27_R1_001.fastq.gz
RNA degraded


title: DSP-1001660015357-A-C04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C04_AHFYT3DSX5

value: breast cancer

value: ER-Neg


title: A2_contra_CAM

description:
Library name: S593_02_A2_contra_S26_R1_001.fastq.gz
-


title: RNA-seq, P5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 2

description:
Library name: TTX2.HALO.RNA
TTX2-RNA-seq

value: TTX


title: DSP-1001660015357-A-C01_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C01_AHFYT3DSX5

value: Stroma


title: DSP-1001660015357-A-B12_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B12_AHFYT3DSX5


title: RNA-seq, P5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, cLTP, rep 2

description:
Library name: cLTP2.HALO.RNA
cLTP2-RNA-seq


title: RK_R+_3T3L1_siRK

description: Library name: sample12

value: WT


title: RNA-seq, P5 mice Organotypic hippocampus slice culture, EGFP-L10a, Ha-GFPnanobody-HALO-PEST, TTX, rep 1

description:
Library name: TTX1.HALO.RNA
TTX1-RNA-seq


title: DSP-1001660015357-A-B11_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B11_AHFYT3DSX5

value: ER-Lo


title: DSP-1001660015357-A-C02_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-C02_AHFYT3DSX5

value: ER-Hi


title: Plasma_cells_1Mek2_rep2

city: Québec

first: Jean

last: Charron

state: QC

address: 2260, boul. Henri-Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

institute: CRCHU de Québec-Université Laval

description:
Library name: 636P
100bp

data_processing:
Reads were trimmed with the software Trim Galore (v0.6.5;https://github.com/FelixKrueger/TrimGalore)
Trimmed reads were mapped to NCBI GRCm39 (mm39) with the software STAR (v2.7.11a) (Dobin et al., Bioinformatics 2013).
Read counts extraction were made with the mm39 genome with FeatureCounts (v2.0.3; Liao et al., Bioinformatics 2014).
Counts were normalized in TPM ( transcripts per million)
Assembly: NCBI GRCm39 (mm39)
Supplementary files format and content: Tab_delimited text file include raw counts for each Sample
Supplementary files format and content: Tab_delimited text file include TPM for each Sample

source_name: Plasma cell

growth_protocol: 3 to 5 months mice were used to isolate the splenocytes

extract_protocol:
mRNA were isolated by polyA selection from 500ng to 1000 ng of total RNA. Library were made using Illumina TruSeq RNA prep kit
RNA-seq

treatment_protocol: The spleen was gently mashed on a 70-μm nylon strainer to generate a single cell suspension. Cell collection was performed in PBS 2% BSA and filtered through a 70-μm nylon strainer. Cell purification was performed by cell sorting after labeling with the fluorochrome-conjugated antibodies against B220, CD93, CD138, GL7, FAS, CD21 and CD23.

value: Plasma cell


title: DSP-1001660015357-A-B10_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B10_AHFYT3DSX5


title: Cd200r1 knockout 3

first: Marisa

last: Brake

address: 3 Blackfan Cir

institute: Beth Israel Deaconess Medical Center

description: Library name: K3

data_processing:
Raw reads of fastq format were firstly processed through the Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: mm39
Supplementary files format and content: tab-delimited text file including the FPKM and differential expression analysis for each sample

source_name: Whole liver

extract_protocol:
RNA was extracted using the Qiagen Rneasy Plus Universal Mini Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for a directional library.

value: Whole liver

value: F


title: Cd200r1 knockout 2

description: Library name: K2


title: Plasma_cells_1Mek2_rep3

description:
Library name: 654P
100bp


title: Cd200r1 knockout 4

description: Library name: K4


title: Plasma_cells_1Mek2_rep1

description:
Library name: 323P
100bp


title: F2_pos

description: Library name: S540_12_Post_F2_pos

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Bulk RNA-seq data was aligned with STAR v2.7.11a to the mouse reference genome Gencode M33. Counts were obtained using FeatureCounts v2.0.6. Data was analyzed using DESeq2 1.46.0.
Assembly: Gencode M33
Supplementary files format and content: Processed counts are provided in the file Counts_Mrc1creERT2_repopulation.txt

source_name: Brain without choroid plexuses

extract_protocol:
Cells were sorted into RNAprotect Cell Reagent (QIAGEN) according to the manufacturers recommendations. Total RNA was extracted from FACS sorted cells stabilized in RNAprotect Cell Reagent according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAprotect at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAprotect was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 seconds. Genomic DNA contamination was removed by using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added, and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, the total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
Library preparation and RNAseq were carried out as described in the SMART-Seq mRNA LP User Manual (Takara Bio, Inc., CA, USA), the Illumina NextSeq 2000 Sequencing System Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism Protocol (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). In brief, approximately 500 pg of total-RNA was used to generate first strand cDNA. Double stranded cDNA was amplified by LD-PCR (13 cycles) and purified via magnetic bead clean-up. After validating the quality and quantity, 250 pg of cDNA was enzymatically fragmented and stem-loop adapters were ligated. Then libraries were PCR amplified (16 cycles) and indexed, generating Illumina-compatible libraries with unique dual indexes (UDIs). After a magnetic bead purification, the libraries were quantified using the KAPA Library Quantification Kit. Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1. 5.0.42699, using two 100 cycles P2 Flow Cells with the dual index, single-read (SR) run parameters.

treatment_protocol: Mice were injected with Tamoxifen and treated four weeks later either treated for seven consectutive days with either Vehicle solution (CTL) or BLZ945. Cells were harvested 8 weeks after the end of the treatment.

value: Brain without choroid plexuses

value: BLZ945 200 mg/kg for 7 days 8 weeks before sorting


title: F2_neg

description: Library name: S540_11_Post_F2_neg


title: DSP-1001660015357-A-B09_AHFYT3DSX5

first: Fangyuan

last: Chen

institute: Dana-Farber Cancer Institute

description: Library name: DSP-1001660015357-A-B09_AHFYT3DSX5


title: A2_ipsi_CAM

description:
Library name: S593_01_A2_ipsi_S25_R1_001.fastq.gz
-

value: Veh


title: DSP-1001660015357-A-B08_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B08_AHFYT3DSX5


title: DSP-1001660015357-A-B07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B07_AHFYT3DSX5


title: Wildtype 4

description: Library name: C4

value: wildtype


title: S-pattern_rep1

value: adenoma


title: Plasma_cells_wt_rep1

description:
Library name: 358P
100bp

value: wt


title: DSP-1001660015357-A-B06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B06_AHFYT3DSX5


title: Cd200r1 knockout 1

description: Library name: K1


title: M2_pos

description: Library name: S540_08_Post_M2_pos

value: CAMs


title: F1_pos

description: Library name: S540_10_Post_F1_pos


title: Marginal_zone_B_cells_1Mek2_rep3

description:
Library name: 654M
100bp

source_name: Marginal zone B cell

value: Marginal zone B cell


title: DSP-1001660015357-A-B05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B05_AHFYT3DSX5

source_name: breast cancer

value: breast cancer


title: Marginal_zone_B_cells_1Mek2_rep2

description:
Library name: 634M
100bp


title: M2_neg

description: Library name: S540_07_Post_M2_neg


title: Wildtype 2

description: Library name: C2


title: Plasma_cells_wt_rep2

description:
Library name: 412P
100bp


title: Plasma_cells_wt_rep3

description:
Library name: 487P
100bp


title: M1_neg

description: Library name: S540_05_Post_M1_neg


title: DSP-1001660015357-A-B04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B04_AHFYT3DSX5

value: ER-Neg


title: Marginal_zone_B_cells_1Mek2_rep1

description:
Library name: 323M
100bp


title: 3D_to_2D_P2_2

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

description:
Library name: 3D_to_2D_P2_2
mouse_stem_cell_count.txt

data_processing:
Low-quality RNA sequencing reads and adapters were removed by cutadapt v1.11 and then the clean reads were aligned to human cDNA database (hg19) using HISAT2(v2.2.1). The gene counts was calculated with gene annotation from UCSC database using FeatureCounts (v2.0.1)
Assembly: hg19 for human cells and mm9 for mouse cells
Supplementary files format and content: txt format; count

source_name: mfPSCs

extract_protocol:
Bulk-RNA seq: Total RNA was isolated cells using TRIzol® Reagent (MRC, Cat# RN 190). Genomic DNA (gDNA) contamination was eliminated from the total RNA by the digestion of RQ1 DNase (Promega, Cat# M610A) for 1 h at 37 °C. RNA integrity was verified by Bioanalyzer 2100 (Agilent Technologies) with RNA Integrity Number (RIN) > 8.0.
Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; Add Fragmentation Buffer for mRNA fragmentation; One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; PCR enrichment was performed to obtain cDNA libraries.RNA-seq libraries were sequenced on Illumina NovaSeq X paktform.

value: mfPSCs

value: mPSCs


title: Wildtype 1

description: Library name: C1


title: M2_CTL

description: Library name: S540_04_pre_M2_CTL

value: Vehicle 7 days 8 weeks before sorting


title: Marginal_zone_B_cells_wt_rep3

description:
Library name: 562M
100bp


title: DSP-1001660015357-A-B02_AHFYT3DSX5

address: 450 Brookline Avenue

description: Library name: DSP-1001660015357-A-B02_AHFYT3DSX5

value: ER-Hi


title: Wildtype 3

description: Library name: C3


title: F1_neg

description: Library name: S540_09_Post_F1_neg


title: Marginal_zone_B_cells_wt_rep1

description:
Library name: 412M
100bp


title: DSP-1001660015357-A-B01_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B01_AHFYT3DSX5

value: Stroma


title: DSP-1001660015357-A-B03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-B03_AHFYT3DSX5

value: ER-Lo


title: Marginal_zone_B_cells_wt_rep2

description:
Library name: 358M
100bp


title: M1_CTL

description: Library name: S540_03_pre_M1_CTL


title: 3D_to_2D_P1_2

description:
Library name: 3D_to_2D_P1_2
mouse_stem_cell_count.txt


title: DSP-1001660015357-A-A12_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A12_AHFYT3DSX5


title: M1_pos

description: Library name: S540_06_Post_M1_pos


title: Follicular_B_cells_1Mek2_rep4

description:
Library name: 713F
100bp

source_name: Follicular B cell

value: Follicular B cell


title: F2_CTL

description: Library name: S540_02_pre_F2_CTL

value: Brain without choroid plexuses


title: Follicular_B_cells_1Mek2_rep3

description:
Library name: 654F
100bp


title: sample 2 of liver constituent cells from a wild-type male mouse treated with CCl4

description:
Library name: CCl4_2
BD Rhapsody

data_processing:
To generate a fastq file for each sample, raw sequence reads were demultiplexed using splitBarcode v2.0.0 (MGI Tech). Primary quality control was performed in the Seven Bridge pipeline using FASTQ files and mouse genome annotation files (GRCm38).
Assembly: GRCm38
Supplementary files format and content: comma-separated values files containing cell barcodes and Gene Expression Counts

extract_protocol:
After liver perfusion with pronase (#107433; Sigma‒Aldrich) and collagenase (#C5138; Sigma‒Aldrich), hepatocytes were removed via low-speed centrifugation (50 × g). The percentage of viable cells in the cell suspension was greater than 70%, and approximately 10,000 viable cells were used for library preparation.
For the construction of the scRNA-seq library, a cDNA Kit and Whole Transcriptome Analysis (WTA) Amplification Kit (Becton Dickinson and Co., Franklin Lakes, NJ) were used according to the manufacturer’s instructions. Rhapsody WTA libraries were sequenced on the DNBSEQ-G400RS platform (MGI Tech).

treatment_protocol: Male mice aged 8 to 10 weeks were injected intraperitoneally with 10 μl/g body weight CCl4 in a 1:9 ratio with corn oil or corn oil twice a week for 5 weeks. The mice were sacrificed and analyzed 48 hours after the last injection.

value: liver

value: liver constituent cells

value: wild


title: 3D_to_2D_P1_1

description:
Library name: 3D_to_2D_P1_1
mouse_stem_cell_count.txt


title: 3D_to_2D_P2_1

description:
Library name: 3D_to_2D_P2_1
mouse_stem_cell_count.txt


title: F1_CTL

description: Library name: S540_01_pre_F1_CTL


title: DSP-1001660015357-A-A11_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A11_AHFYT3DSX5


title: DSP-1001660015357-A-A10_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A10_AHFYT3DSX5


title: sample 1 of liver constituent cells from a wild-type male mouse treated with CCl4

description:
Library name: CCl4_1
BD Rhapsody


title: ATAC-seq_lhys_ZT36_1

first: Hao

last: Tian

address: 105 West Third Ring Road North, Haidian District, Beijing,

institute: Capital normal university

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC and aligned to the glycine max v2.1 reference genome using Bowtie2, and sorted and indexed using samtool.
Model based analysis of ChIP-seq (MACS) used for peak calling.Or got the bigwig file afted downsample and merge.
Assembly: Ws82v2.1
Supplementary files format and content: narrowpeak and bigwig

organism: Glycine max

source_name: first tri-foliate leaf

growth_protocol: Wild-type (WT) soybean (Glycine max (L.) Mer. Willimas82 (Ws82)) seedlings were grown under SD conditions (8 h light / 16 h dark) for about 18 days with temperature cycles of 24 °C (light) / 22 °C (dark), until the first tri-foliate leaf open.

extract_protocol:
Approximately 0.5 g of soybean mature leaves were used in each experiment. About 1 to 2g of the sample was ground into a fine powder in liquid nitrogen.
For ATAC-seq, 50 k Isolated soybean nuclei were prepared for chromatin digestion by Tn5 transposase (VAHTS; cat. no. TD501) for 30 min at 37 °C. Digested chromatin was purified using a 2xCTAB followed by PCR amplification, product purification (vazyme, N411) and paired- end sequencing (2 ×150 bp) using an Illumina Hiseq X-Ten.

treatment_protocol: On the nineteenth day, the plants were transferred into LL (constant light, 25°C). After one day under LL, first tri-foliate leaf were sampled every 4 h for 20 h starting at ZT0 on the 21th day for RNA-seq, ATAC-seq and ChIP-seq under free-running conditions. 3 biological replicates were obtained for each time point.

value: first tri-foliate leaf

tag: cultivar

value: lhys mutant

value: free-running


title: ATAC-seq_lhys_ZT36_2


title: ATAC-seq_luxs_ZT36_2

value: luxs mutant


title: sample 2 of liver constituent cells from a wild-type male mouse treated with corn oil

description:
Library name: control_2
BD Rhapsody

value: corn oil


title: ATAC-seq_luxs_ZT36_1


title: Follicular_B_cells_1Mek2_rep1

description:
Library name: 634F
100bp


title: Follicular_B_cells_1Mek2_rep2

description:
Library name: 636F
100bp


title: sample 1 of liver constituent cells from a wild-type male mouse treated with corn oil

description:
Library name: control_1
BD Rhapsody


title: ATAC-seq_Ws82_ZT36_2


title: sample 3 of liver constituent cells from a wild-type male mouse after pIVCL, treated with CWHM-12

description:
Library name: treatment 3
BD Rhapsody

data_processing:
To generate a fastq file for each sample, raw sequence reads were demultiplexed using splitBarcode v2.0.0 (MGI Tech). Primary quality control was performed in the Seven Bridge pipeline using FASTQ files and mouse genome annotation files (GRCm39).
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and count matrix files

extract_protocol:
After liver perfusion with pronase (#107433; Sigma‒Aldrich) and collagenase (#C5138; Sigma‒Aldrich), the cell suspension was conditioned to be 90% liver nonparenchymal cells and 10% hepatocytes, and dead cells and erythrocytes were removed via density gradient centrifugation using Percoll PLUS (GE17-5445-02; Cytiva). The percentage of viable cells in the cell suspension was greater than 70%, and approximately 10,000 viable cells were used for library preparation.
For the construction of the scRNA-seq library, a cDNA Kit and Whole Transcriptome Analysis (WTA) Amplification Kit (Becton Dickinson and Co., Franklin Lakes, NJ) were used according to the manufacturer’s instructions. Rhapsody WTA libraries were sequenced on the DNBSEQ-G400RS platform (MGI Tech).

treatment_protocol: Male mice aged 8 to 10 weeks were subjected topartial inferior vena cava ligation (pIVCL) (Simonetto DA, et al. Hepatology. 2015; 61:648-659), and after 2 weeks, Alzet osmotic pumps containing either the pan-integrin αV inhibitor CWHM-12 (100 mg/kg/day) or vehicle (DMSO) were inserted subcutaneously. At 4 weeks after the start of treatment, the mice were sacrificed and analyzed.

value: wild-type

value: pIVCL, treated with CWHM-12


title: Follicular_B_cells_wt_rep2

description:
Library name: 562F
100bp

value: wt


title: Follicular_B_cells_wt_rep3

description:
Library name: 670F
100bp


title: DSP-1001660015357-A-A07_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A07_AHFYT3DSX5

value: breast cancer


title: DSP-1001660015357-A-A06_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A06_AHFYT3DSX5

value: ER-Hi


title: DSP-1001660015357-A-A05_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A05_AHFYT3DSX5

value: Stroma


title: Follicular_B_cells_wt_rep4

description:
Library name: 671F
100bp


title: sample 2 of liver constituent cells from a wild-type male mouse after pIVCL, treated with CWHM-12

description:
Library name: treatment 2
BD Rhapsody


title: DSP-1001660015357-A-A09_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A09_AHFYT3DSX5


title: Age_associated_B_cells_1Mek2_rep3

description:
Library name: 666ABC
100bp

source_name: Age associated B cell

value: Age associated B cell


title: DSP-1001660015357-A-A04_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A04_AHFYT3DSX5

value: ER-Neg


title: ATAC-seq_Ws82_ZT36_1


title: sample 1 of liver constituent cells from a wild-type male mouse after pIVCL, treated with CWHM-12

description:
Library name: treatment 1
BD Rhapsody


title: Follicular_B_cells_wt_rep1

description:
Library name: 412F
100bp

value: Follicular B cell


title: DSP-1001660015357-A-A08_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A08_AHFYT3DSX5


title: Age_associated_B_cells_1Mek2_rep2

description:
Library name: 654ABC
100bp


title: ATAC-seq_lhys_ZT24_1


title: sample 3 of liver constituent cells from a wild-type male mouse after pIVCL, treated with DMSO

description:
Library name: control 3
BD Rhapsody

value: liver

value: pIVCL, treated with DMSO


title: DSP-1001660015357-A-A02_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A02_AHFYT3DSX5


title: sample 2 of liver constituent cells from a wild-type male mouse after pIVCL, treated with DMSO

description:
Library name: control 2
BD Rhapsody

value: liver constituent cells


title: ATAC-seq_luxs_ZT24_2

value: first tri-foliate leaf


title: Age_associated_B_cells_1Mek2_rep1

description:
Library name: 634ABC
100bp


title: sample 1 of liver constituent cells from a wild-type male mouse after pIVCL, treated with DMSO

description:
Library name: control 1
BD Rhapsody


title: ATAC-seq_lhys_ZT24_2

value: lhys mutant


title: DSP-1001660002557-B-G09_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G09_AH2G7CDSX7


title: Age_associated_B_cells_wt_rep3

description:
Library name: 670ABC
100bp


title: a sample of liver constituent cells from the control WT littermate after pIVCL

description:
Library name: KO
BD Rhapsody

data_processing:
To generate a fastq file for each sample, raw sequence reads were demultiplexed using splitBarcode v2.0.0 (MGI Tech). Primary quality control was performed in the Seven Bridge pipeline using FASTQ files and mouse genome annotation files (GRCm39).
Assembly: GRCm39
Supplementary files format and content: comma-separated values files containing cell barcodes and Gene Expression Counts

extract_protocol:
After liver perfusion with pronase (#107433; Sigma‒Aldrich) and collagenase (#C5138; Sigma‒Aldrich), hepatocytes were removed via low-speed centrifugation (50 × g), and dead cells and erythrocytes were removed via density gradient centrifugation using Percoll PLUS (GE17-5445-02; Cytiva). The percentage of viable cells in the cell suspension was greater than 70%, and approximately 10,000 viable cells were used for library preparation.
For the construction of the scRNA-seq library, a cDNA Kit and Whole Transcriptome Analysis (WTA) Amplification Kit (Becton Dickinson and Co., Franklin Lakes, NJ) were used according to the manufacturer’s instructions. Rhapsody WTA libraries were sequenced on the DNBSEQ-G400RS platform (MGI Tech).

treatment_protocol: The endothelial cell-specific CTGF KO male mouse and  the control WT littermate were subjected to partial inferior vena cava ligation (pIVCL) (Simonetto DA, et al. Hepatology. 2015; 61:648-659).

value: Cdh5-CreERT2; Ctgffl/fl

value: pIVCL


title: DSP-1001660015357-A-A03_AHFYT3DSX5

description: Library name: DSP-1001660015357-A-A03_AHFYT3DSX5

value: ER-Lo


title: ATAC-seq_luxs_ZT24_1

value: luxs mutant

value: free-running


title: DSP-1001660002557-B-G08_AH2G7CDSX7

description: Library name: DSP-1001660002557-B-G08_AH2G7CDSX7


title: ATAC-seq_Ws82_ZT24_2


title: Age_associated_B_cells_wt_rep2

description:
Library name: 562ABC
100bp

value: wt


title: Age_associated_B_cells_wt_rep1

description:
Library name: 412ABC
100bp