title: TCL1tgIkk2hetCD19cre, Spleen, 3 months old, rep4

city: Munich

first: Marc

last: Schmidt-Supprian

state: Bavaria

address: Einsteinstr. 25

department: Tranlational Cancer Research

institute: TUM

description: Library name: TCL1tgIkk2hetCD19cre__SPL_3m_BR4

data_processing:
bcl2fastq
Drop-seq protocol
This dataset was generated using SCRB-Seq for single-cell RNA sequencing of Mus musculus (GRCm38, Gencode M25). Raw BCL files were converted to FASTQ using Bcl2Fastq with adapter masking (13 bp). No trimming was applied. Alignment was performed using STAR (v2.7.5b), and downstream processing utilized Drop-seq Tools (v1.12) and Picard (v2.18.26).  Mapping statistics indicate high alignment rates, with an average of ~88% mapped reads per sample, primarily exonic. Detailed per-sample alignment and processing statistics are included in the submission.
Assembly: GRCm38
Supplementary files format and content: tab delimeted text file contains DGE matrix
Supplementary files format and content: tab delimeted text file contains meta data

source_name: Spleen

extract_protocol:
RNA was isolated from TCL lysate via AmpureXP beads (Beckman Coulter).
Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Fischer et al. 2023). Barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 5'-Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. cDNA from all samples was pooled and amplified with KAPA HiFi ReadyMix (KAPA Biosystems). To obtain sequencing libraries, tagmented and 3’ ends were amplified with the Nextera XT Kit (Illumina). The library was sequenced on a NextSeq 500 (Illumina) with 16 cycles for the barcodes and UMIs in read1 and 51 cycles for the cDNA in read2. Data was processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to GENCODE M25.

treatment_protocol: Splenic and peritoneal single cell suspensions from 2-3 mice per genotype were first stained with the anti-mouse CD16/CD32 monoclonal antibody (eBioscience, 1:200) on ice for 30 minutes. Cells were then stained extracellularly with antibodies against CD19 (Clone eBio1D3), B220 (clone RA3-6B2), IgM (clone II/41), IgD (clone 11-26c/11-26) and CD5 (Clone 53-7.3). For exclusion of dead cells either live-dead dye 7-AAD (eBioscience) or the near-IR dead cell staining kit (Invitrogen) were used. Cells were then resuspended in FACS Buffer (2% heat inactivated FBS in PBS), filtered through a 35 µm nylon mesh (Corning) and sorted for single, living B1a cells (CD5+ B220low CD19+ and eGFP+ for IKK2 mice) with BD FACS Aria™ II, BD FACS Aria™ III or BD FACS Aria™ Fusion. One thousand B1a splenic and peritoneal cells were sorted into each well of a 96-well PCR plate pre-filled with 5µl buffer TCL (Qiagen). When possible, two wells (technical replicates) were sorted for each population. Plates were then sealed, centrifuged and stored at -80°C.

value: Spleen


title: RT112 7 µM Erdafitinib rep1

status: Public on Mar 11 2026

type: SRA

city: Innsbruck

first: Florian

last: Handle

address: Josef-Wilberger-Str. 9a

country: Austria

institute: XPseq Analytics GmbH

description: Library name: RT112 7 uM Erdafitinib rep1

library_source: transcriptomic

data_processing:
Basecalling was performed with dorado (version 1.1.0) using the high accuracy model. Raw sequencing reads were aligned to the human genome (GENCODE Release 47, GRCh38.p14) using the Minimap2 aligner (version 2.28). Read counting was performed with the Rsubread (version 2.22.1).
Assembly: GRCh38
Supplementary files format and content: counts.txt: Tab delimited file containing reads counts for all samples. First column is the ensemble gene identifier.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: UMUC3 cells were cultured in DMEM-low glucose medium. RT112 and 5637 cells were cultured in RPMI 1640 medium. All media were supplemented with 10% fetal calf serum, 1% penicillin/streptomycin, and 1% GlutaMAX. Routine mycoplasma testing was performed for all cell cultures and STR profiling was performed to verify the authenticity of the cell lines.

extract_protocol:
Total RNA was isolated using the FavorPrep Tissue Total RNA purification Mini Kit (FavorGen BioTech Corp.) following the manufacturer’s protocol.
Gene expression analysis was performed using the ExpressoSeq rapid 3' RNA-Seq service (XPseq Analytics GmbH).

treatment_protocol: Cells were seeded in 96 well plates, left to attach for 24 hours before treatment with the EGFR inhibitors neratinib (600 nM) and afatinib (4 µM), the MAPK inhibitor trametinib (2 µM), the FGFR inhibitor erdafitinib (7 µM) or DMSO vehicle for 3 days.

tag: cell line


title: Blood_AD_47

city: Boca Raton

first: Massimo

last: Caputi

address: 777 Glades Road

country: USA

institute: Florida Atlantic University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed 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 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
For lncRNA and mRNA: (Stringtie- 1.3.3b) was used to count the read numbers mapped to each gene. And then FPKM was calculated, which expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced. FPKM is a simple and mostly common used expression level normalization method. It normalizes for both sequencing depth and genome size.
Prior to differential expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Significantly differential expression genes were screened based on the following criteria: Corrected P-value < 0.05.
For circRNA: The circRNA were detected and identified using find_circ (Memczak et al., 2013) and CIRI2 (Gao et al., 2017). The raw counts were first normalized using TPM (Zhou et al., 2010) Normalized expression level = ( readCount* 1,000,000 ) / libsize ( libsize is the sum of circRNA readcount) . Differential expression analysis of the two groups was performed using the DESeq2 R package (1.20.0). 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: ensembl_82_homo_sapiens_grch38_primary
Supplementary files format and content: ADvsControl.lncRNA.transcript_level.deg.txt ; differential expression
Supplementary files format and content: ADvsControl.mRNA.gene_level.deg.txt ; differential expression
Supplementary files format and content: circRNA_ADvsControl_deg.xlsx; differential expression

molecule: total RNA

source_name: Whole Blood

extract_protocol:
The blood was collected in PAXgene Blood RNA tubes. Total RNA was extracted following the protocol developed by this lab to isolate RNAs of different sizes and low concentration (Paz S, Mauer C, Ritchie A, Robishaw JD, Caputi M. A simplified SARS-CoV-2 detection protocol for research laboratories. PLoS One. 2020 Dec 18;15(12):e0244271). RNA sample quality and quantity were determined utilizing an Agilent TapeStation system and a NanoDrop spectrophotometer. The samples utilized for the cDNA library preparations had an RNA integrity number (RIN) ≥ 7 and an RNA concentration ≥ 30 ng/µL. Ribosomal RNA was removed by Epicentre TruSeq Stranded Total RNA Library Prep Gold/illumina/20020599
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, 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 (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. 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 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tissue

value: Whole Blood

tag: disease state

value: AD


title: TCL1tgIkk2hetCD19cre, Spleen, 3 months old, rep14

country: Germany

description: Library name: TCL1tgIkk2hetCD19cre__SPL_3m_BR14

organism: Mus musculus

tag: genotype


title: Blood_AD_46


title: BKS_db_H3K27ac_rep2

city: Guangzhou

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

country: France

institute: Guangdong Provincial People's Hospital

description: Library name: BKS_db_H3K27ac_rep2

library_source: genomic

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

molecule: genomic DNA

source_name: aorta

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

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

value: aorta

tag: cell type

value: Endothelial cell of aorta

tag: treatment


title: XF-6_S6

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description: Library name: XF-6_S6

data_processing:
The raw data was processed through in-house perl scripts.
Paired-end reads were mapped to the mm10 genome with Hisat2 v2.0.5
Assembly: mm10

source_name: mouse bone marrow

extract_protocol:
CD8+ T cells were flow-sorted from BM cells.
Libraries of gene expression of BM CD8+ T cell sequencing for mice were generated using the SMART-Seq mRNA LP kit (Takara Bio, San Jose, CA) .

treatment_protocol: Bone marrow  CD8+ T cells in bone marrow failure (BMF) mice treated with or without baricitinib (BAR) at day 10 and day 14 post BMF induction.

value: mouse bone marrow

value: CD8+ T cells


title: XF-4_S4

description: Library name: XF-4_S4


title: TCL1tgCD19cre, Spleen, 3 months old, rep10

description: Library name: TCL1tgCD19cre_SPL_3m_BR10


title: XF-3_S3

description: Library name: XF-3_S3


title: XF-5_S5

description: Library name: XF-5_S5


title: RT112 0.6 µM Neratinib rep1

description: Library name: RT112 0,6 uM Neratinib rep1


title: TCL1tgCD19cre, Spleen, 9 months old, rep9

description: Library name: TCL1tgCD19cre_SPL_9m_BR9


title: Blood_AD_44


title: Blood_AD_45


title: TCL1tgCD19cre, Spleen, 3 months old, rep7

description: Library name: TCL1tgCD19cre_SPL_3m_BR7


title: XF-2_S2

description: Library name: XF-2_S2


title: Ikk2hom, Spleen, 3 months old, rep 13

description: Library name: Ikk2homCD19cre_SPL_3m_BR13


title: Blood_AD_43


title: RT112 2 µM Trametinib rep1

description: Library name: RT112 2 uM Trametinib rep1


title: RT112 Control rep1

description: Library name: RT112 Control rep1


title: Ikk2hom, Spleen, 3 months old, rep 12

description: Library name: Ikk2homCD19cre_SPL_3m_BR12


title: 5637 7 µM Erdafitinib rep1

description: Library name: 5637 7 uM Erdafitinib rep1


title: XF-1_S1

description: Library name: XF-1_S1


title: 5637 2 µM Trametinib rep1

description: Library name: 5637 2 uM Trametinib rep1


title: Blood_AD_42


title: RT112 4 µM Afatinib rep1

description: Library name: RT112 4 uM Afatinib rep1


title: 5637 4 µM Afatinib rep1

description: Library name: 5637 4 uM Afatinib rep1


title: XF-16_S16

description: Library name: XF-16_S16


title: Blood_AD_40


title: TCL1tgCD19cre, Spleen, 3 months old, rep8

description: Library name: TCL1tgCD19cre_SPL_3m_BR8


title: XF-15_S15

description: Library name: XF-15_S15


title: 5637 0.6 µM Neratinib rep1

description: Library name: 5637 0,6 uM Neratinib rep1


title: XF-13_S13

description: Library name: XF-13_S13


title: Blood_AD_41


title: Blood_AD_38


title: UMUC3 7 µM Erdafitinib rep1

description: Library name: UMUC3 7 uM Erdafitinib rep1


title: 5637 Control rep1

description: Library name: 5637 Control rep1


title: Ikk2het, Spleen, 3 months old, rep5

description: Library name: Ikk2hetCD19cre_SPL_3m_BR5


title: Ikk2hom, Spleen, 3 months old, rep 11

description: Library name: Ikk2homCD19cre_SPL_3m_BR11


title: XF-14_S14

description: Library name: XF-14_S14


title: Control, Spleen, old, rep16

description: Library name: CD19cre_SPL_old_BR16


title: UMUC3 2 µM Trametinib rep1

description: Library name: UMUC3 2 uM Trametinib rep1


title: Control, Spleen, old, rep15

description: Library name: CD19cre_SPL_old_BR15


title: XF-12_S12

description: Library name: XF-12_S12


title: Blood_AD_37


title: XF-11_S11

description: Library name: XF-11_S11


title: Blood_AD_36


title: Ikk2het, Spleen, 3 months old, rep6

description: Library name: Ikk2hetCD19cre_SPL_3m_BR6


title: Blood_AD_35


title: UMUC3 4 µM Afatinib rep1

description: Library name: UMUC3 4 uM Afatinib rep1


title: UMUC3 0.6 µM Neratinib rep1

description: Library name: UMUC3 0,6 uM Neratinib rep1


title: Control, Spleen, 3 month old, rep1

description: Library name: CD19cre_SPL_3m_BR1


title: TCL1tgIkk2hetCD19cre, Peritoneal cavity, 3 months old, rep17

description: Library name: TCL1tgIkk2hetCD19cre__PC_3m_BR17

source_name: Peritoneal cavity

value: Peritoneal cavity


title: UMUC3 Control rep1

description: Library name: UMUC3 Control rep1


title: STZ_control_ATAC_rep3

description: Library name: STZ_control_ATAC_rep3

value: NaCl injection


title: Blood_AD_39


title: STZ_control_ATAC_rep4

description: Library name: STZ_control_ATAC_rep4


title: Blood_AD_33


title: XF-10_S10

description: Library name: XF-10_S10


title: STZ_control_ATAC_rep2

description: Library name: STZ_control_ATAC_rep2


title: Blood_AD_34


title: Control, Spleen, 3 month old, rep2

description: Library name: CD19cre_SPL_3m_BR2


title: TCL1tgIkk2hetCD19cre, Peritoneal cavity, 3 months old, rep8

description: Library name: TCL1tgIkk2hetCD19cre__PC_3m_BR8


title: Blood_AD_31


title: Five Day Dynamic 3D Scaffold, Replicate 2

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10th Amistad Street

department: Department of Anesthesiology

institute: Yale University

description:
Library name: LEP_DL2
10X Genomics

library_source: transcriptomic single cell

data_processing:
For further information on single cell object analysis, including cleaning, normalization and scaling, embedding, annotation, please refer to manuscript methods.
Assembly: Rattus_norvegicus.Rnor_6.0.95
Supplementary files format and content: R objects (.Robj)

organism: Rattus norvegicus

source_name: Bioengineered rat lung (epithelial only), 5 day

growth_protocol: Primary rat lung-derived cells (from pulmonary dissociation) were expanded and reprogrammed in 2D culture with a DMEM F12 supplemented with growth factors (Fgf10, Egf), small molecule inhibitors of TGFβ, p38-MAPK, GSK3 signaling, and antibiotics (LPM-3D). 2D cultures were incubated at 37°C in a humidified atmosphere with 5% CO₂ for 7-10 days before each passage. Passage 0 cells were cultured for 10 days, while all other passages were cultured for 7 days. At passage 4, growth medium was switched to the DCIR+L medium (see manuscript methods). Whole-engineered lungs were seeded using the lung epithelial progenitors from 2D culture. Engineered lungs were cultured in LPM-3D growth medium for 24 hours and then switched to DCIR+L growth medium for the rest of culture (takedown on day 5).

extract_protocol:
Single-cell suspensions were prepared from dissociated native fetal rat lungs, adult native rat lungs, and bioengineered lungs (24 hr and 5 day cultures) a using customized enzymatic solution containing dispase, collagenase, DNase, and elastase in DMEM. Dissociated suspensions were then filtered to achieve a single-cell suspension. 2D cultured cells were lifted with 0.25% trypsin and then quenched with DMEM + 10% FBS. All cells were resuspended in 0.1% BSA in PBS at 1 million cells/mL and processed for single-cell RNA-seq using the Chromium Next GEM Single Cell 3’ v3.1 platform (10x Genomics, Pleasanton, CA), following the manufacturer’s protocol. Cell lysis and mRNA capture occurred within Gel Beads-in-emulsion (GEMs) using barcoded oligo(dT) primers. See manuscript for more detail.
Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits (v3.1) (10x Genomics, Pleasanton, CA), following the manusfacturer's instructions. Barcoded cDNA was amplified by PCR and purified with SPRIselect beads in preparation for sequencing on the Illumina platform. See manuscript methods for additional details.

value: WT


title: Five Day Dynamic 3D Scaffold, Replicate 1

description:
Library name: LEP_DL1
10X Genomics

value: Bioengineered rat lung (epithelial only), 5 day


title: TCL1tgIkk2hetCD19cre, Peritoneal cavity, 3 months old, rep7

description: Library name: TCL1tgIkk2hetCD19cre__PC_3m_BR7


title: Blood_AD_32


title: STZ_control_ATAC_rep1

description: Library name: STZ_control_ATAC_rep1


title: STZ_db_ATAC_rep3

description: Library name: STZ_db_ATAC_rep3

value: Streptozotocin injection


title: Control, Spleen, 3 month old, rep3

description: Library name: CD19cre_SPL_3m_BR3


title: Blood_AD_29


title: TCL1tgCD19cre, Peritoneal cavity, 9 months old, rep9

description: Library name: TCL1tgCD19cre_PC_9m_BR9


title: STZ_db_ATAC_rep2

description: Library name: STZ_db_ATAC_rep2


title: 24 Hour Dynamic 3D Scaffold, Replicate 3

description:
Library name: BDL3
10X Genomics

source_name: Bioengineered rat lung (epithelial only), 24 hour


title: TCL1tgCD19cre, Peritoneal cavity, 9 months old, rep12

description: Library name: TCL1tgCD19cre_PC_9m_BR12


title: Blood_AD_30


title: Five Day Dynamic 3D Scaffold, Replicate 3

description:
Library name: LEP_DL3
10X Genomics


title: STZ_db_ATAC_rep1

description: Library name: STZ_db_ATAC_rep1


title: Blood_AD_28


title: TCL1tgCD19cre, Peritoneal cavity, 3 months old, rep5

description: Library name: TCL1tgCD19cre_PC_3m_BR5


title: 24 Hour Dynamic 3D Scaffold, Replicate 2

description:
Library name: BDL2
10X Genomics

value: Bioengineered rat lung (epithelial only), 24 hour


title: TCL1tgCD19cre, Peritoneal cavity, 3 months old, rep3

description: Library name: TCL1tgCD19cre_PC_3m_BR3


title: Ikk2hom, Peritoneal cavity, 3 months old, rep 16

description: Library name: Ikk2homCD19cre_PC_3m_BR16


title: C57BL6_control_ATAC_rep2

description: Library name: C57BL6_control_ATAC_rep2

value: Normal diet


title: Blood_AD_26


title: Passage 3 2D Culture, Replicate 2

description:
Library name: P3-2
10X Genomics

source_name: Pulmonary epithelial cells, 2D culture

value: Pulmonary epithelial cells, 2D culture


title: C57BL6_control_ATAC_rep1

description: Library name: C57BL6_control_ATAC_rep1


title: Ikk2hom, Peritoneal cavity, 3 months old, rep 13

description: Library name: Ikk2homCD19cre_PC_3m_BR13


title: Blood_AD_27


title: Ikk2hom, Peritoneal cavity, 3 months old, rep 14

description: Library name: Ikk2homCD19cre_PC_3m_BR14


title: 24 Hour Dynamic 3D Scaffold, Replicate 1

description:
Library name: BDL1
10X Genomics


title: Passage 3 2D Culture, Replicate 3

description:
Library name: P3-3
10X Genomics


title: C57BL6_control_ATAC_rep3

description: Library name: C57BL6_control_ATAC_rep3


title: Passage 3 2D Culture, Replicate 1

description:
Library name: P3-1
10X Genomics


title: C57BL6_db_ATAC_rep3

description: Library name: C57BL6_db_ATAC_rep3

value: High fat diet


title: Passage 0 2D Culture, Replicate 3

description:
Library name: P0-3
10X Genomics


title: C57BL6_db_ATAC_rep2

description: Library name: C57BL6_db_ATAC_rep2


title: Blood_AD_25


title: Ikk2het, Peritoneal cavity, 3 months old, rep15

description: Library name: Ikk2hetCD19cre_PC_3m_BR15


title: Blood_AD_24


title: Ikk2het, Peritoneal cavity, 3 months old, rep1

description: Library name: Ikk2hetCD19cre_PC_3m_BR1


title: Passage 0 2D Culture, Replicate 2

description:
Library name: P0-2
10X Genomics


title: Passage 0 2D Culture, Replicate 1

description:
Library name: P0-1
10X Genomics


title: Blood_AD_23


title: BKS_control_ATAC_rep2

description: Library name: BKS_control_ATAC_rep2


title: Blood_AD_22


title: Blood_AD_21


title: Embryonic Day 19 Sample 1

description:
Library name: NRL19
10X Genomics

source_name: Native fetal rat lung, E19

value: Native fetal rat lung, E19


title: BKS_db_ATAC_rep2

description: Library name: BKS_db_ATAC_rep2


title: Control, Peritoneal cavity, old, rep19

description: Library name: CD19cre_PC_old_BR19


title: Ikk2het, Peritoneal cavity, 3 months old, rep6

description: Library name: Ikk2hetCD19cre_PC_3m_BR6


title: Embryonic Day 17 Sample 1

description:
Library name: frl1
10X Genomics

source_name: Native fetal rat lung, E17

value: Native fetal rat lung, E17


title: BKS_control_ATAC_rep1

description: Library name: BKS_control_ATAC_rep1


title: C57BL6_db_ATAC_rep1

description: Library name: C57BL6_db_ATAC_rep1


title: Blood_AD_19

value: Whole Blood


title: Rat Sciatic Nerve Repair Using PLLARS Conduit With Ultrasound: Sample 3

city: Beijing

first: Haofeng

last: Cheng

state: Beijing

address: No.28 Fuxing Road

country: China

institute: Chinese PLA General Hospital

description: Library name: PLLARS_US_3

data_processing:
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3).The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples. Thousands of independent statistical hypothesis testing was conducted on DEGs, separately. Then a p-value was obtained, which was corrected by FDR method. And Corrected P-value (q-value) was calculated by correcting using BH method. p-value or q-value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and p ≤ 0.05.
The annotation of the DEGs were perfomed based on the information obtained from the database of ENSEMBL, NCBI, Uniprot, GO, and KEGG.
Assembly: hg38
Supplementary files format and content: xlsx files included FPKM value of each sample.

source_name: sciatic nerve

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen). Total RNA samples that meet the following requirements were used in subsequent experiments: RNA integrity number (RIN) > 7.0 and a 28S:18S ratio > 1.8.RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).
The triplicate samples of all assays were constructed an independent library, and do the following sequencing and analysis. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer. After quantitative reverse transcription-polymerase chain reaction (RT-qPCR) validation, libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina NovaSeq sequencer (Illumina).

treatment_protocol: The PLLARS_US group was treated with PLLARS conduits and received ultrasound stimulation, while the PCL group was treated with PCL conduits without ultrasound stimulation.

value: sciatic nerve

value: PLLARS Conduit With Ultrasound


title: Embryonic Day 17 Sample 2

description:
Library name: frl2
10X Genomics


title: BKS_db_ATAC_rep1

description: Library name: BKS_db_ATAC_rep1

value: aorta

value: Endothelial cell of aorta


title: Blood_AD_18

value: AD


title: Control, Peritoneal cavity, old, rep10

description: Library name: CD19cre_PC_old_BR10

value: Peritoneal cavity


title: Control, Peritoneal cavity, 3 month old, rep11

description: Library name: CD19cre_PC_3m_BR11


title: Blood_AD_17


title: Rat Sciatic Nerve Repair Using PLLARS Conduit With Ultrasound: Sample 2

description: Library name: PLLARS_US_2


title: GFP+ P14 CD8 T cells, CRIPSR, rep_5 of of LCMV Cl13 SPL

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
Guide-derived oligonucleotide (GDO)
CRISPR library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads

library_source: other

data_processing:
CellRanger v4.0.0. muliranger functions to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. In Seurat, viable cells were filtered and integrated seurat objectives were generated for Arm and Cl13 infection.
Assembly: mm10
Supplementary files format and content: Seurat Objective: Chung_2024_Cl13_Perturb_seq.rds, 5 biological replicates combined
Supplementary files format and content: Seurat Objective: Chung_2024_Arm_Perturb_seq.rds, 3 biological replicates combined
Library strategy: CITE-seq

molecule: other

extract_protocol:
Cas9 transgenic P14 cells were transduced with gRNA and transferred in LCMV Armstrong or Clone 13 strain infected animal (day 1). On day 18+ of post-infection, T cells were harvested from spleen and/or small intestine. GFP positive P14 CD8 T cells were FACS sorted and single cells were encapsulated in gel-beads-in emulson (GEMs) uising the 10X Controller with a Chromium Single Cell 5' GEM Libarary and Gel Bead kit.
Chromium GEM-X Single Cell 5' Reagent Kits v3 with Feature Barcode technology for CRISPR Screening & Cell Surface Protein

value: Spleen

value: CD8+ T cells

value: LCMV Clone13 D18+

tag: library type

value: GDO


title: Control, Peritoneal cavity, 3 month old, rep4

description: Library name: CD19cre_PC_3m_BR4


title: P7_WT_Hippocampus

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

description:
Library name: 3285-RG-07
10X Genomics

data_processing:
10x Genomics CellRanger software version 7.0.1
Seurat version 4.0.5 implemented in R version 4.1.2
Nuclei were excluded if they had fewer than 500 or more than 7,500 unique features
data were integrated with GSE186216 and normalized following a standard Seurat  SCTransform+CCA integration pipeline
Principal component analysis was performed on the top 3000 variable genes and the top 25 principal components were used for downstream analysis. The Louvain algorithm was used with resolution set to 0.5 to group cells together
Assembly: 10X supplied mm10-2020-A
Supplementary files format and content: standard 10X Genomics count data

source_name: Hippocampus

extract_protocol:
P7 WT mouse hippocampi were micro-dissected and tissue homogenized with a dounce homogenizer in ice-cold EZ PREP buffer (Nuclei isolation kit, Sigma # NUC101-1KT). Samples were briefly centrifuged, rinsed, and resuspended in buffer containing 0.1% RNase inhibitor (Roche, #03335399001). After filtering through a 40 µm cell strainer, the number of nuclei was counted using a hemocytometer
we used the Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (Dual Index). Barcoding and library preparation was performed following the manufacturer’s protocols. Briefly, to generate single-nuclei gel-bead in-emulsion (GEMs) solution, approximately 15,000 nuclei, in a final volume of 43 µl, were loaded on a Next GEM Chip G (10x Genomics) and processed with the 10x Genomics Chromium Controller. Reverse transcription was performed as follows: 53°C for 45 minutes and 85°C for 5 minutes in a Veriti Therml Cycler (Applied Biosystems). Next, first-strand cDNA was cleaned with DynaBeads MyOne SILANE (10x Genomics, 2000048). The amplified cDNA and final libraries were prepared and cleaned with SPRIselect Regent kit (Beckman Coulter, B23318).  Libraries were pooled for sequencing with a NovaSeq 6000 (Illumina) at an estimated depth of 50,000 reads per nucleus.

value: Hippocampus

value: WT

tag: age


title: Blood_AD_20


title: Blood_AD_16


title: GFP+ P14 CD8 T cells, GEX, rep_5 of of LCMV Cl13 SPL

description:
polyA RNA
GEX library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: Control, Peritoneal cavity, old, rep18

description: Library name: CD19cre_PC_old_BR18


title: Control, Peritoneal cavity, 3 month old, rep2

description: Library name: CD19cre_PC_3m_BR2


title: Blood_AD_15


title: Rat Sciatic Nerve Repair Using PLLARS Conduit With Ultrasound: Sample 1

description: Library name: PLLARS_US_1


title: Rat Sciatic Nerve Repair Using PCL Conduit Without Ultrasound: Sample 3

description: Library name: PCL_3

value: PCL Conduit Without Ultrasound


title: Rat Sciatic Nerve Repair Using PCL Conduit Without Ultrasound: Sample 2

description: Library name: PCL_2


title: Blood_AD_14


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 32878

description: Library name: S-CLL-32878_TCL1tgIkk2hetCD19cre_6m

data_processing:
bcl2fastq
Drop-seq protocol
This dataset was generated using SCRB-Seq for single-cell RNA sequencing of Mus musculus (GRCm38, Gencode M25). Raw BCL files were converted to FASTQ using Bcl2Fastq with adapter masking (13 bp). No trimming was applied. Alignment was performed using STAR (v2.7.5b), and downstream processing utilized Drop-seq Tools (v1.12) and Picard (v2.18.26).  Mapping statistics indicate high alignment rates, with an average of ~79% mapped reads per sample, primarily exonic. Detailed per-sample alignment and processing statistics are included in the submission.
Assembly: GRCm38
Supplementary files format and content: tab delimeted text file contains DGE matrix
Supplementary files format and content: tab delimeted text file contains meta data

extract_protocol:
RNA was isolated from the RLT lysate with the RNeasyPlus kit (Qiagen).
Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Fischer et al. 2023). Barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 5'-Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. cDNA from all samples was pooled and amplified with KAPA HiFi ReadyMix (KAPA Biosystems). To obtain sequencing libraries, tagmented and 3’ ends were amplified with the Nextera XT Kit (Illumina). The library was sequenced on a NextSeq 500 (Illumina) with 16 cycles for the barcodes and UMIs in read1 and 51 cycles for the cDNA in read2. Data was processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to GENCODE M25.

treatment_protocol: Single cell suspension from the spleen of 5-12 tumorigenic mice were first stained with the anti-mouse CD16/CD32 monoclonal antibody (eBioscience, 1:200) on ice for 30 minutes. B1a cells were purified either by sorting (CD19+ B220lo CD5+, and eGFP+ in the case of IKK2ca mice) or enriched by MACS negative depletion (Miltenyi). Sorted tumorigenic B1a cells were stained extracellularly with antibodies against  CD19 (Clone eBio1D3), B220 (clone RA3-6B2), IgM (clone II/41), IgD (clone 11-26c/11-26) and CD5 (Clone 53-7.3). For exclusion of dead cells either live-dead dye 7-AAD (eBioscience) or the near-IR dead cell staining kit (Invitrogen) were used. Cells were then resuspended in FACS Buffer (2% heat inactivated FBS in PBS), filtered through a 35 µm nylon mesh (Corning) and sorted for single, living B1a cells (CD5+ B220low CD19+ and eGFP+ for IKK2ca mice) with BD FACS Aria™ II, BD FACS Aria™ III or BD FACS Aria™ Fusion. The maximum number of cells possible were sorted per sample. MACS enriched B1a cells were manually magnetically purified by staining cells with a cocktail of biotinylated antibodies (Gr1+ clone RB6-8C5, Ter119+ clone Ter119, CD3+ clone 145-2C11, F4/80+ clone CI:A3-1, CD11c+ clone N418 and IL7R+/CD127 clone A7R34) followed depletion of the stained cells using anti-Biotin magnetic beads (Miltenyi) and the LS-columns (Miltenyi), according to the manufacturer’s instructions. Negative enrichment purity of the population of interest was validated by flow cytometry comparing before and after fractions. Samples were centrifuged, supernatant was carefully removed and samples were immediately lysed in up to 5 million cells per 350µl RLT lysis buffer and stored at -80°C.


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 31306

description: Library name: S-CLL-31306_TCL1tgIkk2hetCD19cre_6m


title: GFP+ P14 CD8 T cells, GEX, rep_4 of of LCMV Cl13 SPL


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 20503

description: Library name: S-CLL-20503_TCL1tgIkk2hetCD19cre_6m


title: GFP+ P14 CD8 T cells, HTO, rep_4 of of LCMV Cl13 SPL

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

molecule: protein

value: HTO

tag: hto

value: HTO-3:LCMV Cl13 SPL rep4


title: Rat Sciatic Nerve Repair Using PCL Conduit Without Ultrasound: Sample 1

description: Library name: PCL_1


title: RNA-seq of rat spinal cord (pooled)

city: Heidelberg

first: Alexander

last: Younsi

address: INF 400

department: Neurosurgery

institute: Heidelberg University Hospital

description:
Library name: AWT_bulkRNA
Contains pooled barcoded spinal cord RNA from 9 rats (3 SHAM, 3 SCI+Vehicle, 3 SCI+IL-4); see processed data files for group separation.

data_processing:
Reads were quality-checked and aligned to the Rattus norvegicus reference genome using STAR. Gene-level count matrices were generated with featureCounts. Differential expression analysis was performed in Scanpy using Wilcoxon rank sum tests and adjusted p-values via Benjamini-Hochberg correction. Pathway enrichment was performed using clusterProfiler with GO and KEGG databases. All samples were multiplexed and sequenced together; reads were demultiplexed using sample-specific barcodes during processing.
Assembly: Rnor_6.0
Supplementary files format and content: Processed data includes: matrix.mtx.gz (raw count matrix), features.tsv.gz (gene annotations), and barcodes.tsv.gz (sample barcodes). Format follows the 10x-style sparse matrix convention.

source_name: Spinal Cord

growth_protocol: Rats were perfused with 1x PBS at 4°C, spinal cords were extracted and snapfrozen

extract_protocol:
Rat spinal cords were stored and shipped in sCelLive® Tissue Preservation Solution (Singleron Biotechnologies GmbH). RNA was isolated with the GeneMAtrix Universal RNA Purification Kit (Roboklon) and subsequently processed according to the instructions of the AccuraCode® RNA-Seq kit (Singleron Biotechnologies GmbH)
Total RNA was extracted using the GeneMAtrix Universal RNA Purification Kit (Roboklon). mRNA was captured with AccuraCode® bulk beads (Singleron Biotechnologies GmbH) and reverse transcribed into cDNA with sample-specific barcodes and unique molecular identifiers (UMIs). Libraries were constructed with the AccuraCode® RNA-Seq Kit (Singleron Biotechnologies GmbH) and sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp).

treatment_protocol: We used a thoracic clip contusion-compression injury model. Of 120 rats in the experiment, 30 were randomized to a sham group receiving laminectomy at T10 only, 45 were assigned to i. p. IL-4 treatment and 45 to the vehicle group with i. p. saline treatment. Rats received i. p. injections for up to seven days after SCI twice daily. The current tissue was treated for 72h and extracted 72 hours after injury

value: Spinal Cord


title: Blood_AD_13

value: Whole Blood


title: GFP+ P14 CD8 T cells, CRIPSR, rep_3 of of LCMV Cl13 SPL


title: Blood_AD_12


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 01140

description: Library name: S-CLL-01140_TCL1tgIkk2hetCD19cre_6m


title: Rat hepatocytes , 2 weeks after IR, P-STAT3 (ChIP)

city: cahgnzhou

first: Wendong

last: Gu

address: NO.185, juqianjie road

institute: The Third Affiliated Hospital of Soochow University

description: Library name: Liver_trans

data_processing:
Deep sequencing was subsequently performed on the Illumina NovaSeq 6000 platform with a 150-base-pair paired-end configuration.
Raw data (raw reads) of fastq format were firstly processed through 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.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 was used to call peaks with qvalue < 0.05.The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.Peaks were annotated by ChIPseeker package.
Assembly: Rat (Rattus norvegicus) reference genome (Rnor_6.0)
Supplementary files format and content: bigWig

source_name: Liver

growth_protocol: DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Hepatocytes were isolated from SD rats using two-step collagenase perfusion. Briefly, the liver was first perfused in situ with Ca²⁺-free HBSS at a perfusion rate of 5 mL/min. The samples were subsequently perfused sequentially with HBSS containing 1.3 mmol/L CaCl2 and collagenase I (Worthington) for 20 minutes. The liver was then removed and placed in HBSS. The capsule was incised to release the digested hepatocytes. The resulting cell suspension was filtered through a 70-mm filter. The cell suspension was centrifuged at 40 ×g for 3 minutes. The supernatant was discarded, and the sediment at the bottom included the primary hepatocytes. Cell viability was confirmed using a trypan blue exclusion assay.
These cells were then crosslinked with 1% formaldehyde at room temperature for 10 minutes. After sonication, immunoprecipitation was performed with a p-STAT3 (Tyr705) antibody (Cell Signaling Technology, #9145). The immunoprecipitated complex was subsequently washed. The DNA was then extracted and purified with the MinElute PCR Purification Kit (QIAGEN, #28006). To prepare the ChIP-Seq library, the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, #TD501) was utilized following the manufacturer’s instructions. In the case of ChIP-seq, the extracted DNA was first ligated to specific adaptors.

treatment_protocol: Irradiation of 30 Gy on the right upper quadrant of the abdomen

value: Liver

value: Hepatocyte

value: Irradiation of 30 Gy

tag: chip antibody

value: P-STAT3 (Tyr705) (Cell Signaling Technology, #9145)


title: GFP+ P14 CD8 T cells, HTO, rep_3 of of LCMV Cl13 SPL

value: HTO-2:LCMV Cl13 SPL rep3


title: Blood_AD_11

value: AD


title: GFP+ P14 CD8 T cells, CRIPSR, rep_4 of of LCMV Cl13 SPL

value: Spleen

value: CD8+ T cells


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 33180-2

description: Library name: S-CLL-33180-2_TCL1tgCD19cre_9m


title: GFP+ P14 CD8 T cells, GEX, rep_3 of of LCMV Cl13 SPL

value: LCMV Clone13 D18+


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 01139

description: Library name: S-CLL-01139_TCL1tgIkk2hetCD19cre_6m


title: Rat hepatocytes , 2 weeks after IR, P-STAT3 (Input)

description: Library name: Liver_Input


title: Blood_AD_10


title: Blood_AD_9


title: liver, 30 Gy, 2 weeks after treat, rep3

description:
Library name: Radiation_3
BD Rhapsody system

data_processing:
The sequencing reads were aligned using the CellRanger software package (v3.0.2).
Assembly: Rat (Rattus norvegicus) reference genome (Rnor_6.0)
Supplementary files format and content: h5ad files

extract_protocol:
Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 1 mg/mL collagenase I (Gibco)，1 mg/mL collagenase II，60U/mL Hyaluronidase (Sigma), 10U/mL Liberase (Roche) and 0.02mg/mL DNase I (Roche) for 90 min at 37°C, with agitation . After digestion, samples were sieved through a 100µm and 40µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Gibco) to lyse red blood cells. After washing with DPBS containing sample buffer, the cell pellets were re-suspended in DPBS containing sample buffer，stained and counted.
BD Rhapsody system was used to capture the transcriptomic information of the liver single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity D1000 ScreenTape (Agilent）and High Sensitivity D1000 Reagents (Agilent）on a 4150 TapeStation System (Agilent) and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

tag: strain

value: Sprague-Dawley

tag: Sex

value: male


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 02499

description: Library name: S-CLL-02499_TCL1tgCD19cre_9m


title: GFP+ P14 CD8 T cells, CRIPSR, rep_2 of of LCMV Cl13 SPL

value: GDO


title: Blood_AD_8


title: GFP+ P14 CD8 T cells, HTO, rep_2 of of LCMV Cl13 SPL

value: HTO-1:LCMV Cl13 SPL rep2


title: liver, 30 Gy, 2 weeks after treat, rep2

description:
Library name: Radiation_2
BD Rhapsody system


title: GFP+ P14 CD8 T cells, GEX, rep_2 of of LCMV Cl13 SPL

value: mRNA


title: Spleen, Tumor sample, Ikk2homCD19cre, age: 9m, sample: 01775

description: Library name: S-CLL-01775_Ikk2homCD19cre_9m


title: liver, 30 Gy, 2 weeks after treat, rep1

description:
Library name: Radiation_1
BD Rhapsody system


title: liver, 0 Gy, 2 weeks after treat, rep3

description:
Library name: Control_3
BD Rhapsody system

value: Irradiation of 0 Gy


title: GFP+ P14 CD8 T cells, CRIPSR, rep_3 of LCMV Arm SPL, rep_1 of LCMV Cl13 SPL

value: LCMV Armstrong D18+, LCMV Clone13 D18+


title: Blood_AD_5

value: Whole Blood


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 31835

description: Library name: S-CLL-31835_TCL1tgIkk2hetCD19cre_6m


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 20501

description: Library name: S-CLL-20501_TCL1tgIkk2hetCD19cre_6m


title: liver, 0 Gy, 2 weeks after treat, rep1

description:
Library name: Control_1
BD Rhapsody system

value: Liver


title: GFP+ P14 CD8 T cells, GEX, rep_3 of LCMV Arm SPL, rep_1 of LCMV Cl13 SPL

description:
polyA RNA
GEX library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: liver, 0 Gy, 2 weeks after treat, rep2

description:
Library name: Control_2
BD Rhapsody system


title: Blood_AD_3


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 00425

description: Library name: S-CLL-00425_TCL1tgCD19cre_9m


title: Blood_AD_2


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 02970

description: Library name: S-CLL-02970_TCL1tgIkk2hetCD19cre_6m


title: GFP+ P14 CD8 T cells, HTO, rep_3 of LCMV Arm SPL, rep_1 of LCMV Cl13 SPL

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: HTO

value: HTO-3:LCMV Arm SPL rep3, HTO-8:LCMV Cl13 SPL rep1


title: GFP+ P14 CD8 T cells, CRISPR, rep_1 of LCMV Arm SPL, rep_2 of LCMV Arm SPL

description:
Guide-derived oligonucleotide (GDO)
CRISPR library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads

value: LCMV Armstrong D18+


title: H628CBm_ATAC

first: Yuting

last: Liu

state: CT

address: 333 Cedar Street

institute: YALE UNIVERSITY

description: Library name: H628CBm_ATAC_MAH

library_source: genomic single cell

data_processing:
Raw base call files were converted to FASTQ format and processed using Cell Ranger ARC (v2.0.1, 10x Genomics). Reads were aligned to species-specific reference genomes. Gene expression matrices and chromatin accessibility peak counts were generated using default Cell Ranger ARC parameters. Nuclei were filtered based on quality control thresholds including UMI counts, feature counts, mitochondrial gene percentage (>5%), total ATAC fragment counts (<1,000), and transcription start site enrichment score (<4). Downstream clustering and cell type annotation were performed using Seurat (v4.0.6).
Assembly: human, GRCh38; chimpanzees, panTro5;rhesus macaque, rheMac10; marmoset, calJac4
Supplementary files format and content: cellranger output: feature_bc_matrix.h5
Supplementary files format and content: cellranger output: atac_fragments.tsv.gz

source_name: cerebellum

extract_protocol:
Frozen cerebellar cortex tissue was homogenized and nuclei were isolated using detergent-based resuspension buffers containing NaCl, MgCl₂, Tris-HCl, NP-40, Tween-20, digitonin, protease inhibitors, DTT, BSA, and RNase inhibitor. Nuclei were filtered through 70 µm strainers, centrifuged at 500 × g at 4°C, and resuspended in nuclei buffer supplemented with DTT and RNase inhibitor. Nuclei concentration was adjusted to 4.5 × 10⁶ nuclei/mL prior to microfluidic capture.
Single-nucleus RNA and chromatin accessibility libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC and Gene Expression kit (10x Genomics, PN-1000283) according to the manufacturer’s instructions. Approximately 10,000 nuclei were targeted per sample using the Chromium microfluidic system with Multiome Gel Bead Kit A and Multiome GEM Kit A. RNA and ATAC libraries were generated in parallel from the same nuclei preparation.

value: cerebellum

tag: developmental stage

value: adult

value: ATAC


title: H628CBm_RNA

description: Library name: H628CBm_GEX_MAH

molecule: nuclear RNA


title: Blood_AD_6

value: AD


title: GFP+ P14 CD8 T cells, HTO, rep_1 of LCMV Arm SPL, rep_2 of LCMV Arm SPL

value: Spleen

value: CD8+ T cells

value: HTO-1:LCMV Arm SPL rep1, HTO-2:LCMV Arm SPL rep2


title: Blood_AD_1


title: Spleen, Tumor sample, TCL1tgIkk2homCD19cre, age: 3m, sample: 03286

description: Library name: S-CLL-03286_TCL1tgIkk2homCD19cre_3m


title: GFP+ P14 CD8 T cells, GEX, rep_1 of LCMV Arm SPL, rep_2 of LCMV Arm SPL


title: Spleen, Tumor sample, TCL1tgCg1cre, age: 9m, sample: 02509

description: Library name: S-CLL-02509_TCL1tgCg1cre_9m


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 35359

description: Library name: S-CLL-35359_TCL1tgCD19cre_9m


title: Blood_AD_7


title: Blood_AD_4


title: GFP+ P14 CD8 T cells, HTO, rep_2 of LCMV Arm IEL rep_3 of LCMV Arm IEL

source_name: Small Instestine

value: Small Instestine

value: HTO-2:LCMV Arm IEL rep2, HTO-3:LCMV Arm IEL rep3


title: Spleen, Tumor sample, TCL1tgCD19cre, age: old, sample: 33180-1

description: Library name: S-CLL-33180-1_TCL1tgCD19cre_old


title: Spleen, Tumor sample, Ikk2hetCD19cre, age: old, sample: 34800

description: Library name: S-CLL-34800_Ikk2hetCD19cre_old


title: GFP+ P14 CD8 T cells, GEX, rep_2 of LCMV Arm IEL rep_3 of LCMV Arm IEL

value: mRNA


title: urine RNA, BKVN-P, 7

city: New York

first: Manikkam

last: Suthanthiran

state: New York

address: 1300 York Ave, Rm A569

department: Nephrology and Hypertension

institute: Weill Cornell Medicine

description: Library name: BKV 1868

data_processing:
Illumina Casava1.8 software used for basecalling
Assembly: Sequence reads were aligned to hg38 STAR with default parameters
Supplementary files format and content: FPKM were obtained using CuffLinks

source_name: urine RNA

extract_protocol:
Urine samples were centrifuged at 1250x g for 30 minutes at room temperature, and total RNA was isolated from urinary cells using the RNeasy mini kit (Qiagen) followed by DNase I (Qiagen) treatment.
Illumina TruSeq RNA Sample Library Preparation v2 kit (Illumina)

value: urine RNA

value: BKVN-P

tag: batch


title: H187CBm_ATAC

description: Library name: H187CBm_ATAC_MAH


title: Spleen, Tumor sample, Ikk2hetCD19cre, age: old, sample: 34801

description: Library name: S-CLL-34801_Ikk2hetCD19cre_old

source_name: Spleen


title: PDA83_DM_1

city: THUWAL

first: Samhan

middle: M.

last: Alsolami

address: Thuwal 23955

department: BESE

country: Saudi Arabia

institute: KAUST

data_processing:
The ATAC-seq sequencing raw data were preprocessed with the default parameters by NGmerge to remove adapters and low-quality reads.
The cleaned reads were aligned to the human genome assembly (hg38) using bowtie2 (v.2.3.4.1) with the default parameters except for the following options: “-X 2000 --no-unal --very-sensitive”. Reads mapping to mitochondrial DNA were discarded using the “grep –v chrM” command.
PCA duplicates were removed using the sambamba (v. 0.6.7-pre1) markdup function with “-r” parameters.
The hg38 blacklist regions were removed using “--blackListFileName” parameters.
Peaks were called using MACS2 (v.2.1.1.20160309) with default options except for the following options: “--nomode -f BAMPE --keep-dup all”. ATAC-seq peaks across all samples were merged into one union ATAC-seq peak set using the BEDTools (v.2.26.0) merge function, and ATAC-seq reads in each sample were calculated over the union ATAC-seq peak set using the deepTools (v. 3.5.1) multiBigwigSummary function with bigWig files.
Assembly: hg38
Supplementary files format and content: bed file total peaks

source_name: Pluripotent stem cells

extract_protocol:
Diagenade kit
single indexed library

value: Pluripotent stem cells

value: Induced pluripotent stem cells

value: WT

value: DMSO


title: PDA83_2

value: CTRL


title: Spleen, Tumor sample, Ikk2hetCD19cre, age: old, sample: 00787

description: Library name: S-CLL-00787_Ikk2hetCD19cre_old


title: urine RNA, BKVN-P, 6

description: Library name: BKV 1922


title: H390CBm_RNA

description: Library name: H390CBm_GEX_MAH

value: cerebellum


title: GFP+ P14 CD8 T cells, HTO, rep_1 of LCMV Arm IEL

value: LCMV Armstrong D18+

value: HTO

value: HTO-1:LCMV Arm IEL rep1


title: PXGL_2 (nSC_9N_2)


title: urine RNA, BKVN-P, 5

description: Library name: GEM-UP-1110


title: GFP+ P14 CD8 T cells, CRISPR, rep_2 of LCMV Arm IEL rep_3 of LCMV Arm IEL

value: GDO


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 32357

description: Library name: S-CLL-32357_TCL1tgCD19cre_9m

value: Spleen


title: H390CBm_ATAC

description: Library name: H390CBm_ATAC_MAH

value: adult

value: ATAC


title: Spleen, Tumor sample, Ikk2hetCD19cre, age: old, sample: 00779

description: Library name: S-CLL-00779_Ikk2hetCD19cre_old


title: GFP+ P14 CD8 T cells, GEX, rep_1 of LCMV Arm IEL

value: Small Instestine

value: CD8+ T cells


title: PDA83_DM_2


title: PXGL_1 (nSC_9N_1)


title: urine RNA, BKVN-P, 4

description: Library name: GEM-UP-4416

value: urine RNA


title: N2B27_DM_2


title: PDA83_1


title: H187CBm_RNA

description: Library name: H187CBm_GEX_MAH

value: mRNA


title: Intestinal tumor tissue,Control

city: Shanghai

first: Yingru

last: Zhang

state: Shanghai

address: No. 528, Zhangheng Road, Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine Shuguang Hospital

description: An intestinal tumor tissue from a mouse without chronic stress

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Intestinal tumor

growth_protocol: The human CRC cell line CT26 was cultured in RPMI 1640 medium and maintained in a 37°C humidified incubator with 5% CO2.

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

treatment_protocol: Forty BALB/c mice were randomly divided into a control group and a CUMS group. The mice were treated with CUMS as a model from 4 weeks of age for 2 consecutive months. In the third week, 30 μL of CT26 cell suspension at a concentration of 1×108 cells/mL was injected into the rectal mucosa of each mouse. After the experiment, 2 mice were randomly selected from each group to collect fresh intestinal tumor tissues from the mice.

value: Intestinal tumor

value: Control

tag: time

value: 2 month


title: N2B27_DM_1

value: Pluripotent stem cells

value: Induced pluripotent stem cells

value: WT


title: urine RNA, BKVN-P, 1

description: Library name: U4

value: BKVN-P


title: urine RNA, BKVN-P, 2

description: Library name: U3


title: Spleen, Tumor sample, TCL1tgIkk2homCD19cre, age: 3m, sample: 03108

description: Library name: S-CLL-03108_TCL1tgIkk2homCD19cre_3m


title: Spleen, Tumor sample, TCL1tgIkk2homCD19cre, age: 3m, sample: 32274

description: Library name: S-CLL-32274_TCL1tgIkk2homCD19cre_3m


title: urine RNA, BKVN-P, 3

description: Library name: U1


title: urine RNA, BKVN-N, 4

description: Library name: GEM-UP-4507

value: BKVN-N


title: GFP+ P14 CD8 T cells, CRISPR, rep_1 of LCMV Arm IEL

value: LCMV Armstrong D18+


title: Spleen, Tumor sample, TCL1tgIkk2homCD19cre, age: 3m, sample: 20064

description: Library name: S-CLL-20064_TCL1tgIkk2homCD19cre_3m


title: Y25_NesGrnOE-koBG_7794

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

data_processing:
Sequence reads were processed using Qiagen's software CLC Genomics workbench (v21.0.5) with CLC's default settings for RNA-Seq analysis (Quality parameter set to 0.05).
Trimmed reads were aligned to GRCm38/mm 10 genome. Expression values were generated for each gene or transcript and expressed as total counts, RPKM, TPM and TMM (CPM) normalized counts. TMM reads were used for further analyses of differential gene or transcript expression. Processed data files are provided for gene expression (GE) and transcript expression (TE) for all genes/transcripts and for valid genes where low expression gene had been filtered out.
TMM gene expression valuses were used for further analyses. Gene were filtered to remove low abundant genes. Processed valid genes with TMM values are presented in the third "processed data" file.
Alignment to GRCm38/mm 10 genome
TMM read normalization
Assembly: mm10
Supplementary files format and content: Expression BrowserEGFL7PGRN GE anno - Gene expression total reads, RPKM, TPM and TMM values for each gene
Supplementary files format and content: Expression Browser EGFL7PRGN TE, Transcript expression total reads, RPKM, TPM and TMM values for each transcript
Supplementary files format and content: GE TMM EGFL7PGRN_validgenes: tab delimited txt file of GE TMM normalized reads of valid genes (low expression genes filtered out)

source_name: Brain cortex

growth_protocol: Mice were maintained in the animal housing facility of the Goethe University Frankfurt, with free access to food and water, a 12h/12h dark-light circadian cycle, room temperature of 21-24°C and humidity of 40-65%. During behavioral experiments mice were kept in a Scantained or in IntelliCages. Mice were monitored throughout life for body weights and general health. Female mice were used because the behavioral tests included a long-term experiment in IntelliCages (16 in a large cage) of old mice.

extract_protocol:
The brain was removed, cerebellum, olfactory bulb nad brainstem removed, cut sagittal, one half for RNAseq was immediately frozen in liquid nitrogen and stored at -80° before RNA extraction. Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer. 200 ng of total RNA was send to Novogene (Cambridge, UK) for library preparation and sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. This method is known as polyA-tailed mRNA enrichment. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The workflow of library construction was as follows: mRNA enrichment, fragmentation, reverse transcription, second strand cDNA synthesis, end repair & A-tailing, adapter ligation, size selection, PCR amplification. Barcoded mRNA seq libraries were prepared from 200 ng total RNA.  mRNA was randomly fragmented and cDNA synthesis proceeded through the use of random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain was finished, the second chain was synthesized with the addition of an Illumina buffer. With this and together with the presence of dNTPs, RNase H and polymerase I from E.coli, the second chain was obtained by Nick translation. The resulting products went through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size were enriched by PCR, where indexed P5 and P7 primers were introduced, and final products were purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms on Illumina Novaseq 6000 platform, according to effective library concentration and data amount. Sequencing strategy was paired-end 150 cycles (PE150).

treatment_protocol: No treatment

value: Brain cortex

value: female

tag: age (weeks)

value: NesGrnOE-KOBG

tag: group

value: NesGrnOE-koBG


title: Y28_NesGrnOE-koBG_7891


title: N2B27_2

tag: cell line

value: CTRL


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 20271

description: Library name: S-CLL-20271_TCL1tgIkk2hetCD19cre_6m

tag: tissue

value: Spleen


title: impPALLY_SI_D4

city: barcelona

first: aintzane

last: rueda

state: Choose State

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

country: Spain

institute: Sequentia Biotech SL.

description:
impPALLY_SI_barcodes.tsv
impPALLY_SI_features.tsv
impPALLY_SI_matrix.mtx

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

source_name: postimplantation human blastoids

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

value: embryonic

value: postimplantation human blastoids

value: control


title: impPALLY_SI_D3


title: Y27_NesGrnOE-koBG_7821


title: Y26_NesGrnOE-koBG_7811


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 01147

first: Marc

last: Schmidt-Supprian

address: Einsteinstr. 25

institute: TUM

description: Library name: S-CLL-01147_TCL1tgIkk2hetCD19cre_6m


title: urine RNA, BKVN-N, 2

description: Library name: GEM-UP-5176

value: urine RNA


title: urine RNA, BKVN-N, 3

description: Library name: GEM-UP-4852


title: Y24_NesGrnOE-koBG_7802


title: Y23_NesGrnOE-koBG_7796


title: Spleen, Tumor sample, TCL1tgIkk2homCD19cre, age: 3m, sample: 32897

description: Library name: S-CLL-32897_TCL1tgIkk2homCD19cre_3m


title: impPALLY_SI_D1


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 01145

description: Library name: S-CLL-01145_TCL1tgIkk2hetCD19cre_6m


title: Y22_NesGrnOE-koBG_7820


title: urine RNA, BKVN-N, 1

description: Library name: U5


title: N2B27_1


title: impPALLY_SI_D2


title: LG_JUNB-KD_RNAseq_rep2

description: Library name: LG_JUNB-KD_RNAseq_rep2

source_name: umbilical vein

value: umbilical vein

value: Endothelial cell of umbilical vein


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 34246

description: Library name: S-CLL-34246_TCL1tgCD19cre_9m


title: Y20_Grnflfl_7943

value: Grnflfl


title: PALLY_SI_D3

description:
PALLY_SI_barcodes.tsv
PALLY_SI_features.tsv
PALLY_SI_matrix.mtx

source_name: preimplantation human blastoids

value: preimplantation human blastoids


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 35124

description: Library name: S-CLL-35124_TCL1tgCD19cre_9m


title: PALLY_SI_D2


title: Y18_Grnflfl_7757


title: PALLY_SI_D1


title: Spleen, Tumor sample, TCL1tgCD19cre, age: 9m, sample: 01551

description: Library name: S-CLL-01551_TCL1tgCD19cre_9m


title: Y19_Grnflfl_7761


title: impPALLY_DM_SI_D3

description:
impPALLY_DM_SI_barcodes.tsv
impPALLY_DM_SI_features.tsv
impPALLY_DM_SI_matrix.mtx

source_name: postimplantation human blastoids + DMSO

value: DMSO


title: impPALLY_DM_SI_D4


title: LG_shNull_RNAseq_rep1

description: Library name: LG_shNull_RNAseq_rep1


title: Sal-OVA 1

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: 10X Genomics

data_processing:
Fastq files were processed using cellranger version 5.0.1 with reference refdata-cellranger-mm10-3.0.0.
DropletUtils version 1.18.1 (66) was used for cell calling. emptyDrops() function with parameter by.rank = 17000.  Droplets with fdr < 0.01 were called as cells for samples Sal-MOG1 and Sal-OVA 1-3;  fdr < 0.0001 was used for Sal-MOG 2 and 3.
Clustering was performed using Seurat version 4.3.0
Putative multiplets were removed in each sample separately using scDblFinder version 1.12.0. Further, scran version 1.26.2 was used for adaptive outlier detection within each sample.
Ambient RNA contamination was quantified and corrected using SoupX version 1.6.2
Differential gene expression analysis was performed using DESeq2 version 1.38.3
Supplementary files format and content: CellRanger output files, as tab separated value files or MatrixMarket files.
Supplementary files format and content: figure3a_supp_table.csv: comma separated value file showing cell metadata for cells retained after QC and used in the article

source_name: mesenteric lymph node

extract_protocol:
mesenteric lymph nodes were extracted 3 weeks post colonization
Single cell suspensions of the mesenteric lymph node were processed according to the manufacturer's protocol (3' kit, 10 x genomics)

treatment_protocol: TCRMOG (2D2) animals were mono-colonized with Salmonella expressing either MOG or OVA

value: mesenteric lymph node

value: 7 weeks

value: tg/wt

value: mono-colonized with Salmonella OVA


title: Sal-OVA 3

description: 10X Genomics


title: Spleen, Tumor sample, TCL1tgIkk2hetCD19cre, age: 6m, sample: 00897

city: Munich

description: Library name: S-CLL-00897_TCL1tgIkk2hetCD19cre_6m


title: Y17_Grnflfl_7760

value: Brain cortex

value: female


title: Y16_Grnflfl_7942


title: LG_JUNB-KD_RNAseq_rep1

description: Library name: LG_JUNB-KD_RNAseq_rep1

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

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


title: Y21_Grnflfl_7759


title: impPALLY_DM_SI_D2


title: HG_RBBP6-KD_RNAseq_rep1

description: Library name: HG_RBBP6-KD_RNAseq_rep1

value: JUNB overexpressed

value: high glocose


title: PALLY_SI_D4

value: embryonic


title: HG_Ctrl_RNAseq_rep2

description: Library name: HG_Ctrl_RNAseq_rep2

value: WT


title: HG_RBBP6-KD_RNAseq_rep2

description: Library name: HG_RBBP6-KD_RNAseq_rep2


title: Y14_Grnflfl_7758


title: Sal-MOG 3

description: 10X Genomics

value: mono-colonized with Salmonella MOG


title: LG_shNull_RNAseq_rep2

description: Library name: LG_shNull_RNAseq_rep2


title: Y15_Grnflfl_7753


title: HG_Ctrl_RNAseq_rep1

description: Library name: HG_Ctrl_RNAseq_rep1


title: PALLY_DM_SI_D4

description:
PALLY_DM_SI_barcodes.tsv
PALLY_DM_SI_features.tsv
PALLY_DM_SI_matrix.mtx

source_name: preimplantation human blastoids + DMSO


title: Sal-OVA 2

description: 10X Genomics


title: Y13_PGRNko_Q193

value: PGRN KO x E7koElla-CREneg

value: PGRNko


title: Sal-MOG 2

description: 10X Genomics


title: PALLY_DM_SI_D3


title: Sal-MOG 1

description: 10X Genomics


title: LG_Ctrl_RNAseq_rep1

description: Library name: LG_Ctrl_RNAseq_rep1

value: umbilical vein

value: Endothelial cell of umbilical vein

value: low glucose


title: Y11_PGRNko_Q185


title: PALLY_DM_SI_D2

value: preimplantation human blastoids

value: DMSO


title: Y12_PGRNko_Q084


title: impPALLY_DM_SI_D1

value: postimplantation human blastoids


title: PALLY_DM_SI_D1


title: MEF cells, siBPGM hyperosmolar 5

city: Berlin

first: Robert

last: Labes

address: Charitéplatz 1

department: Institute of Translational Physiology

institute: Charité - Universitätsmedizin Berlin

data_processing:
CLC Genomics Workbench v 21.0.4 with default settings
Reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum read length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2).
They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs.
Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton's UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen).
Trimmed reads were then mapped to the Mouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 gene annotation.

source_name: MEF

growth_protocol: MEF cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: QIAseq UPX 3’ Transcriptome Kit (QIAGEN) according to the manufacturers instruction

value: MEF

value: embryonic fibroblast

value: BPGM knockdown

value: hyperosmosis


title: Y10_PGRNko_Q186

value: Brain cortex

value: female


title: MEF cells, siBPGM hyperosmolar 3


title: HG_JUNB-OE_RNAseq_rep2

first: Lei

last: Jiang

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description: Library name: HG_JUNB-OE_RNAseq_rep2


title: MEF cells, siBPGM hyperosmolar 4


title: N2B27_DMSO_2_DAY3

data_processing:
AIR sequentia
Supplementary files format and content: FPKM

source_name: stem cells

extract_protocol:
We've used RNAeasy qiagen kit
outsourced to Novogene for library constructions
directional library prepARA

value: stem cells

value: Pluripotent stem cells

value: Induced pluripotent stem cells


title: HG_JUNB-OE_RNAseq_rep1

description: Library name: HG_JUNB-OE_RNAseq_rep1

value: WT


title: MEF cells, siBPGM hyperosmolar 2


title: HG_Null_RNAseq_rep2

description: Library name: HG_Null_RNAseq_rep2


title: Y09_EGFL7-PGRNdko_Q173

value: PGRN KO x E7koElla-CREpos


title: LG_Ctrl_RNAseq_rep2

description: Library name: LG_Ctrl_RNAseq_rep2

value: umbilical vein


title: HG_Null_RNAseq_rep1

description: Library name: HG_Null_RNAseq_rep1

value: Endothelial cell of umbilical vein


title: N2B27_2_DAY3

value: CTRL


title: MEF cells, siBPGM hyperosmolar 1


title: N2B27_DMSO_1_DAY3


title: Y08_EGFL7-PGRNdko_Q031


title: LG_Null_RNAseq_rep2

description: Library name: LG_Null_RNAseq_rep2

value: low glucose


title: LG_Null_RNAseq_rep1

description: Library name: LG_Null_RNAseq_rep1


title: MEF cells, mock hyperosmolar 5


title: Y06_EGFL7-PGRNdko_Q125


title: Y07_EGFL7-PGRNdko_Q132


title: MEF cells, mock hyperosmolar 4


title: PDA83_DMSO_2_DAY3

value: DMSO


title: MEF cells, mock hyperosmolar 3


title: PDA83_DMSO_1_DAY3


title: Y04_PGRNko_7894

value: PGRN KO

value: PGRNko


title: N2B27_1_DAY3


title: RNA-seq of Control DLD-1 cells - Rep2 - Lane3

city: GuangZhou

first: Mingzhe

last: Huang

address: Guangzhou, Guangdong

institute: Sun Yat-sen University

description: Library name: Ctrl-2-mRNA-seq_L3

data_processing:
Reads were aligned to the human genome (GRCh38) using HISAT2 (version 2.2.1) with parameters: --rna-strandness RF.FeatureCounts (version 2.0.0) was used to count reads mapped to gene features.DESeq2 (version 1.34.0) was applied to identify differentially expressed genes.
Assembly: Human genome assembly GRCh38 (hg38) was used for read alignment.
Supplementary files format and content: BAM Files: Contain aligned reads mapped to the human genome (GRCh38). Read Counts: Tab-delimited text files listing the number of reads mapped to each gene. Differential Expression: CSV files with gene expression levels and statistical results from DESeq2 analysis, including log-fold changes and p-values.

source_name: Colon

extract_protocol:
For each sample, approximately 1×10^7 cells were washed twice with ice-cold PBS containing 100 µg/mL cycloheximide (Adooq, 66-81-9). Cells were lysed in 1 mL of pre-chilled lysis buffer.The cell lysate was centrifuged at 14,000 rpm for 10 minutes at 4°C, and the supernatant was collected. Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Invitrogen, 12204021) according to the manufacturer’s instructions. RNA quality and quantity were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).
Total RNA was enriched for poly(A)+ mRNA using oligo(dT) beads (Invitrogen, 61002). Strand-specific libraries were generated using the VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme, NR612-02), with fragmentation at 92°C for 180 seconds and a 12-cycle PCR amplification.

value: Colon

value: Colon cancer cells

value: Control


title: RNA-seq of Control DLD-1 cells - Rep2 - Lane1

description: Library name: Ctrl-2-mRNA-seq_L1


title: MEF cells, mock hyperosmolar 2

value: MEF

value: embryonic fibroblast

value: hyperosmosis


title: Y05_EGFL7-PGRNdko_Q294

value: Brain cortex

value: female


title: RNA-seq of Control DLD-1 cells - Rep1 - Lane3

description: Library name: Ctrl-1-mRNA-seq_L3

value: WT


title: PDA83_1_DAY3

value: stem cells

value: Pluripotent stem cells

value: Induced pluripotent stem cells


title: Y03_PGRNko_7819


title: MEF cells, mock hyperosmolar 1


title: PDA83_2_DAY3

value: CTRL


title: MEF cells, siBPGM control 5

value: BPGM knockdown

value: control


title: A83_DMSO_2_DAY3

value: DMSO


title: Y02_PGRNko_7893

value: PGRN KO

value: PGRNko


title: RNA-seq of Control DLD-1 cells - Rep1 - Lane1

description: Library name: Ctrl-1-mRNA-seq_L1

value: Colon

value: Colon cancer cells


title: RNA-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep2 - Lane3

description: Library name: 6-61A-2-mRNA-seq_L3

value: TRMT6/TRMT61A overexpression


title: RNA-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep2 - Lane1

description: Library name: 6-61A-2-mRNA-seq_L1


title: Y01_PGRNko_7892


title: rCDX2_R123 OE in mESC RNA-seq rep2

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: MES_CDX2_rnaseq_featureCount_10samples_rep2.txt

data_processing:
STAR (v2.7.0d) was used to align the RNA-seq reads to mouse genome (mm10) with gene annotation. FeatuerCounts (v1.5.3) was used to count the read number of each gene (with parameters -T 12 -s 2 -p -g gene_name).
Fastp (v0.19.5) was first used to trimmed and removed low quality ATAC-seq reads and adapter sequences (-a CTGTCTCTTATA --detect_adapter_for_pe -w 12 --length_required 20 -q 30). Reads were aligned to mouse reference genome (hg38) using Bowtie2 v2.3.4.3 with parameters (-p 12 -X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom scripts. Sambamba (v0.7.0) was then used to sort the reads and remove duplicates. MACS2 was used to call peaks
paired-end ChIP-seq reads were first trimmed to remove adapter sequences using cutadapt v2.6 (-a AGATCGGAAGAG -A AGATCGGAAGAG -m 20 -q 30). Reads were aligned to mouse reference genome (mm10) using Bowtie2 v2.3.4.3 with parameters (-X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom script. Picard (v2.6.0, http://broadinstitute.github.io/picard/) was then used to sort the reads and remove duplicates.  MACS2 was used to call peaks (-g mm --keep-dup all -q 0.05 -B).
Genome_build: mm10
Supplementary_files_format_and_content: txt, read count

source_name: mESC

extract_protocol:
(a) Total RNA were extracted from all the treated cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).; (b) For ATAC-seq, samples were washed and then lysed in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501).; (c) The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST, 56383)
(a) Truseq Stranded mRNA sequencing libraries were prepared with 2 μg total RNA according to the manufacturer’s protocol (Yeasen 12300ES24). (b) For ATAC-seq, PCR was then performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411). (c) ChIP-seq libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607)

value: mESC

tag: genotype/variation

value: rCDX2_R123 OE


title: MEF cells, siBPGM control 4

value: MEF

value: embryonic fibroblast

tag: genotype


title: A83_DMSO_1_DAY3

tag: cell type

value: WT


title: RNA-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep1 - Lane3

description: Library name: 6-61A-1-mRNA-seq_L3

tag: treatment


title: A83_2_DAY3

value: stem cells


title: A83_1_DAY3

value: Pluripotent stem cells


title: PD_DMSO_2_DAY3

value: Induced pluripotent stem cells


title: MEF cells, siBPGM control 2


title: rCDX2_R13 OE in mESC RNA-seq rep2

value: rCDX2_R13 OE


title: rCDX2_R23 OE in mESC RNA-seq rep2

value: rCDX2_R23 OE


title: RNA-seq of TRMT6/61A-overexpressing DLD-1 cells - Rep1 - Lane1

description: Library name: 6-61A-1-mRNA-seq_L1


title: MEF cells, siBPGM control 1

value: BPGM knockdown

value: control


title: H3K27ac HiChIP of mouse microglia, MCAO Day 6

city: Yushima, Bunkyo-ku

first: Jun

last: Tsuyama

state: Tokyo

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

description:
Library name: HiCHIP_Day6_H3K27ac
H3K27ac HiChIP of FACS-sorted CD45(int)CD11b(int) microglia from mouse brain on day 6 after stroke onset. Sequenced on Illumina HiSeq 4000.

data_processing:
HiChIP paired-end reads were aligned to the mm10 genome using the HiC-Pro 3.1.0 pipeline of default settings.
The peak file was prepared by expanding ATAC-seq signals to 1 kb that were obtained and merged from ATAC-seq analysis of CD45(int)CD11b(int) cells collected from sham-operated and post-ischemic day 6 mice.
Significant loops were called from the peak file and the validPairs file filtered by HiC-Pro using FitHiChIP(S) (bin size: 10,000, low distance threshold: 10,000, high distance threshold: 1,000,000).
Assembly: mm10 (GRCm38)
Supplementary files format and content: ValidPairs: HiC-Pro output text file containing valid interaction pairs. Interactions BED: FitHiChIP output file with significant chromatin interactions.
Library strategy: HiChIP

source_name: brain

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

extract_protocol:
Sham-operated mice or mice after MCAO were transcardially perfused with saline, and then the forebrain was removed. After homogenization with RPMI-1640, 1 mg ml–1 collagenase (Sigma-Aldrich) and 50 mg ml–1 DNase I (Sigma-Aldrich) were added to the homogenates. Brain homogenates were digested for 25 min and subjected to Percoll (GE Healthcare) gradient centrifugation. From the interlayer between 37% and 70% Percoll, cells were isolated and stained with anti-CD45 FITC (30-F11, eBioscience), anti-CD11b PerCP-Cy5.5 (M1/70, eBioscience), and anti-CD31 PE/Cyanine7 (390, eBioscience). The cells were sorted using a FACSAria III cell sorter (BD/Thermo Fisher Scientific).
CD45(int)CD11b(int) cells (200,000–300,000 cells from the sham-operated or ischemic hemisphere) were analyzed by HiChIP according to the protocol described elsewhere. After cells were sonicated for 2 min using a Covaris S220 ultrasonicator (Covaris), 2 µg of antibody against H3K27ac (Abcam, ab4729) and 20 µl of protein A beads (Thermo Fisher) were added to capture the chromatin-antibody complex. Captured chromatin was removed from protein A beads and purified by DNA Clean & Concentrator (Zymo, D4013) to be quantified by Qubit 3.0 (Thermo Fisher). After treatment with Tn5 transposase (Illumina, Nextera DNA Library Preparation Kit) for fragmentation and tagging, the library was prepared by amplification PCR (14 cycles) followed by the purification using SPRI select. Libraries were sequenced on Illumina HiSeq 4000.

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

value: brain

value: microglia

value: wild-type

value: MCAO


title: PD_DMSO_1_DAY3

value: DMSO


title: H3K27ac HiChIP of mouse microglia, sham surgery

description:
Library name: HiCHIP_Sham_H3K27ac
H3K27ac HiChIP of FACS-sorted CD45(int)CD11b(int) microglia from sham-operated mouse brain. Sequenced on Illumina HiSeq 4000.

value: Sham surgery


title: rCDX2_R12 OE in mESC RNA-seq rep2

value: mESC

value: rCDX2_R12 OE


title: MEF cells, mock control 5

value: MEF

value: embryonic fibroblast


title: MEF cells, siBPGM control 3


title: rCDX2_R2 OE in mESC RNA-seq rep2

value: rCDX2_R2 OE


title: PD_2_DAY3

value: stem cells

value: Pluripotent stem cells

value: WT

value: CTRL


title: rCDX2_R3 OE in mESC RNA-seq rep2

value: rCDX2_R3 OE


title: MEF cells, mock control 4

value: control


title: rCDX2_R1 OE in mESC RNA-seq rep2

value: rCDX2_R1 OE


title: BKS_control_RNAseq_rep2

city: Guangzhou

description: Library name: BKS_control_rep2

source_name: aorta

value: aorta

value: Endothelial cell of aorta


title: nSC_9N_2_DAY0

value: Induced pluripotent stem cells


title: MEF cells, mock control 3


title: BKS_db_RNAseq_rep2

description: Library name: BKS_db_rep2


title: BKS_control_RNAseq_rep1

description: Library name: BKS_control_rep1


title: nSC_9N_1_DAY0


title: PD_1_DAY3


title: MEF cells, mock control 2


title: BKS_db_RNAseq_rep1

description: Library name: BKS_db_rep1


title: MEF cells, mock control 1


title: rCDX2 OE in mESC RNA-seq rep2

value: rCDX2 OE


title: Rat lung tissues, IRI, 3

status: Public on Mar 10 2026

city: guangzhou

first: Haoxiang

last: Yuan

address: 28 Qiaozhong Middle Road, Liwan District

department: Department of Thoracic Surgery and Oncology

institute: The First Affiliated Hospital of Guangzhou Medical University

description: Library name: Sample 3

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Star
count counting
Assembly: mRatBN7.2
Supplementary files format and content: TXT file contain counts for each sample

source_name: Left lung

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

value: Left lung

value: IRI

tag: weight

value: male

tag: disease


title: Rat lung tissues, IRI EVs, 3

description: Library name: Sample 6

value: IRI + Rg3@PACVs with NIR

value: Rg3@PACVs + NIR