title: MSC, Passage 5, transferred from 100kPa substrate to 2kPa substrate after 3 passages, RNA-Seq, rep2

city: Charlottesville

first: Andrew

last: Miller

state: Virginia

address: 415 Lane Rd.

department: Biomedical Engineering

institute: University of Virginia

description: Library name: P5_100T2_4-R2

data_processing:
Sequence reads were trimmed for adaptor sequences and QC metrics assessed using TrimGalore! And FastQC packages, respectively. Reads with Phred quality scores < 20 were excluded from downstream analysis.
Reads were aligned to the rn7 genome assembly using HISAT2 with default parameters.
Tables of raw RNA counts for each gene within each sample were quantified using the FeatureCounts package.
Differentially expressed genes were calculated using the package DESeq2.
Gene annotation was performed using the rn7 RefGene GTF file from Ensembl.
Assembly: rn7
Supplementary files format and content: Table of raw counts for each gene within each sample in CSV file format.

organism: Rattus norvegicus

source_name: bone marrow

growth_protocol: MSCs were subcultured at a seeding density of 2,000 cells/cm² and grown for one week between passages. At 80% confluence, MSCs were detached using trypsin-EDTA (0.25%), resuspended in fresh medium, and seeded onto the respective substrates for passaging and/or experimental use. MSCs were isolated and maintained in α-Minimum Essential Medium (α-MEM) with L-Glutamine and nucleosides, supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin.

extract_protocol:
Cells were lysed using TriZol (Thermo Fischer) and RNA isolated with Qiagen's RNeasy Micro Prep kit. RNA isolates with masses >= 0.5μg and RNA integrity number (RIN) scores >= 9.0 were used to create sequencing libraries.
RNA libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Silicone elastomer substrates (Excellness Biotech SA) were used with elastic moduli of 2 kPa, mimicking soft healthy skin to prevent MF activation, and 100 kPa scar-stiff to promote MSC-to-MF activation. Before use, the substrate surfaces were oxygenated, silanized, and coated with 2 μg/cm² gelatin. MSCs were primed for 3 weeks (1 passage per week) on either soft or stiff substrates. To study mechanical memory, MSCs cultured on 100 kPa and 2 kPa substrates were either stiff-primed (100 kPa) for 3 weeks and then switched to soft substrates (2 kPa) for 2 more weeks, or soft-primed (2 kPa) for 3 weeks and then switched to stiff substrates (100 kPa) for another 2 weeks. MSCs continuously grown 5 weeks on stiff (100 kPa) and soft substrates (2 kPa) served as memory controls.

value: bone marrow

value: mesenchymal stromal cell

value: 100kPa→2kPa substrate

tag: time

value: 5 weeks/passages


title: JH1O_SHLD2_KO_JH1bait_1

status: Public on Apr 09 2026

type: SRA

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

description:
Library name: Sample 52
JH1 bait\, SHLD2 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

library_source: genomic

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

molecule: genomic DNA

organism: Mus musculus

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using VDJ-HTGTS-Seq (Hu et al., 2016)

treatment_protocol: v-Abl transformed pro-B cell lines were cultured in R15 medium and stimulated with 3 uM STI-571 treated for 4 days.

tag: cell line

value: v-Abl transformed pro-B cell line

tag: genotype

tag: treatment

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


city: Cambridge

first: Lei

last: Cui

state: MA

address: 75 Ames st. room 8115b room 8115b

country: USA

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 43
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/-, clone A2, replication 1

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases.
Trimmed reads were aligned to the ENSEMBL GRCh38 reference genome using STAR aligner (v2.5.2b), producing BAM files.
Unique gene-level counts were quantified using featureCounts from the Subread package (v1.5.2), restricted to uniquely mapped reads within annotated exon regions.
Differential gene expression analysis was performed with DESeq2 using the Wald test to calculate p-values and log2 fold-changes. Genes with adjusted p-values < 0.01 and absolute log2 fold-changes > 1 were considered differentially expressed.
Assembly: ENSEMBL GRCh38
Supplementary files format and content: CSV file includes raw gene-level count values for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: iPSC-derived neurons were maintained in Neurobasal Medium supplemented with 1.5% v/v 20% glucose, Glutamax (1:100), MEM-NEAA (1:100), B27 Supplement (1:50), brain-derived neurotrophic factor (BDNF, 10 ng/mL), glial cell line-derived neurotrophic factor (GDNF, 10 ng/mL), and ciliary neurotrophic factor (CTNF, 10 ng/mL).

extract_protocol:
Total RNA was extracted from frozen cell pellets using the Qiagen RNeasy Plus Micro Kit following the manufacturer’s instructions. RNA concentration was measured with the Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was evaluated using the Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB) with poly(A) selection. mRNA was enriched with Oligod(T) beads and fragmented at 94°C for 15 minutes. First- and second-strand cDNA synthesis was followed by end repair, 3’ adenylation, adapter ligation, and PCR enrichment. Libraries were validated using the Agilent TapeStation and quantified via Qubit and qPCR (KAPA Biosystems) before sequencing on the Illumina NovaSeq platform (2×150 bp paired-end).

treatment_protocol: Human iPSCs were transduced with a doxycycline-inducible NGN2 expression construct via TALEN-mediated integration at the AAVS1 safe-harbor locus. Cells were cultured in Induction Medium composed of DMEM/F12, Glutamax (1:100), 1.5% v/v 20% glucose, N2 Supplement (1:100), LDN-193189 (200 nM), SB431542 (10 μM), XAV939 (2 μM), and doxycycline (2 μg/mL) to induce NGN2 expression. After 24 hours, the Induction Medium was refreshed to include zeocin (4 μg/mL) for selection. On Day 4, the medium was replaced with Neuron Medium.

tag: tissue

value: iPSC-derived excitatory neurons

tag: cell type

value: NGN2-induced differentiation

value: Day 56

tag: batch

value: batch 1


title: Sample 21 single cell for microglia sequenced with nextseq

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
Library name: samp21_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cell Ranger v6.1.2, with the refdata-gex-mm10-2020-A Cell Ranger reference (10x Genomics) and with the expected number of cells set based on estimated loading
The downsampleReads command in DropletUtils v1.14.2 was used to downsample all samples to the same number of reads per cell, then the emptyDropsCellRanger command was used to remove empty droplets.
This count matrix was then loaded in R v4.0.3. A Seurat v4.0.0 object was created, cells with less than 200 genes were removed, and the data was LogNormalized with NormalizeData
Variable genes were extracted with FindVariableFeatures, data was scaled with ScaleData, and PCA was run with RunPCA with npcs=60. Dimensionality reduction was performed on the count data with scGBM v0.1.0, using the gbm.sc command with M=25 and subset=50,000, using just the variable genes
Clusters were calculated with the FindNeighbors and FindClusters commands using dims=1:25 and the scGBM reduction
Assembly: mm10
Supplementary files format and content: h5ad containing clustered object

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
For single nuclei data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Nuclei were filtered, washed, and purified through sequential centrifugation steps. The final nuclei suspension was resuspended in RNase inhibitor-containing buffer, filtered, and counted prior to loading for single-nucleus RNA-seq. For single cell data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Cell suspensions were filtered, subjected to debris removal, and microglia were enriched using CD11b magnetic bead-based isolation. Purified cells were resuspended in RNase inhibitor-containing buffer and assessed for viability prior to scRNA-seq.
Single-nucleus and single-cell RNA-seq libraries were generated using the Chromium™ Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) following the manufacturer’s instructions, targeting recovery of up to 10,000 nuclei per sample. For single nucleus data, twenty-four libraries were pooled and sequenced on one NextSeq 500 flow cell and four NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1. For single cell data, twenty-four libraries from different animals were pooled based on molar concentrations and sequenced on one NextSeq 500 flow cell and two NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1.

value: Hippocampus

value: Microglia


title: JH1O_RIF1_KO_JH1bait_3

description:
Library name: Sample 51
JH1 bait\, RIF1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 20 single cell for microglia sequenced with nextseq

description:
Library name: samp20_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


description:
Library name: Sample 42
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/+, replication 6

value: WT


title: JH1O_RIF1_KO_JH1bait_2

description:
Library name: Sample 50
JH1 bait\, RIF1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 5, transferred from 2kPa substrate to 100kPa substrate after 3 passages, RNA-Seq, rep2

description: Library name: P5_2T100_4-R2

value: 2kPa→100kPa substrate


description:
Library name: Sample 41
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/+, replication 5


title: MSC, Passage 5, transferred from 100kPa substrate to 2kPa substrate after 3 passages, RNA-Seq, rep1

description: Library name: P5_100T2_4-R1


title: Sample 19 single cell for microglia sequenced with nextseq

description:
Library name: samp19_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


description:
Library name: Sample 40
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/+, replication 4


description:
Library name: Sample 39
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/+, replication 3


title: JH1O_MDC1_KO_JH1bait_3

description:
Library name: Sample 48
JH1 bait\, MDC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 5, 100kPa substrate, RNA-Seq, rep1

description: Library name: P5_100-R1

value: 100kPa substrate


title: MSC, Passage 5, 100kPa substrate, RNA-Seq, rep2

description: Library name: P5_100-R2


title: MSC, Passage 5, transferred from 2kPa substrate to 100kPa substrate after 3 passages, RNA-Seq, rep1

description: Library name: P5_2T100_4-R1


title: Sample 1 single cell for microglia sequenced with nextseq

description:
Library name: samp1_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


description:
Library name: Sample 38
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/+, replication 2


title: JH1O_RIF1_KO_JH1bait_1

description:
Library name: Sample 49
JH1 bait\, RIF1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_MDC1_KO_JH1bait_2

description:
Library name: Sample 47
JH1 bait\, MDC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 18 single cell for microglia sequenced with nextseq

description:
Library name: samp18_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: MSC, Passage 5, 2kPa substrate, RNA-Seq, rep2

description: Library name: P5_2-R2

value: 2kPa substrate


description:
Library name: Sample 37
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/+, replication 1


title: JH1O_MDC1_KO_JH1bait_1

description:
Library name: Sample 46
JH1 bait\, MDC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 17 single cell for microglia sequenced with nextseq

description:
Library name: samp17_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Sample 16 single cell for microglia sequenced with nextseq

description:
Library name: samp16_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: MSC, Passage 5, 2kPa substrate, RNA-Seq, rep1

description: Library name: P5_2-R1


title: Sample 15 single cell for microglia sequenced with nextseq

description:
Library name: samp15_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


description:
Library name: Sample 36
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7-/-, clone E12, replication 3

value: Day 42


title: JH1O_H2AX_KO_JH1bait_3

description:
Library name: Sample 45
JH1 bait\, H2AX knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 35
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7-/-, clone E12, replication 2


description:
Library name: Sample 34
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7-/-, clone E12, replication 1


title: MSC, Passage 3, 100kPa substrate, RNA-Seq, rep3

description: Library name: P3_100-R3

value: bone marrow

value: 3 weeks/passages


title: JH1O_H2AX_KO_JH1bait_2

description:
Library name: Sample 44
JH1 bait\, H2AX knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 3, 100kPa substrate, RNA-Seq, rep2

description: Library name: P3_100-R2

value: mesenchymal stromal cell


title: MSC, Passage 3, 100kPa substrate, RNA-Seq, rep1

description: Library name: P3_100-R1


description:
Library name: Sample 32
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7-/-, clone B1, replication 2


title: JH1O_ATMi_JH1bait_2

description:
Library name: Sample 41
JH1 bait\, ATMi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 0.25μM ATMi on the second day


title: Sample 13 single cell for microglia sequenced with nextseq

description:
Library name: samp13_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Sample 11 single cell for microglia sequenced with nextseq

description:
Library name: samp11_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


description:
Library name: Sample 33
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7-/-, clone B1, replication 3


title: MSC, Passage 3, 2kPa substrate, RNA-Seq, rep3

description: Library name: P3_2-R3


title: JH1O_ATMi_JH1bait_3

description:
Library name: Sample 42
JH1 bait\, ATMi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: Sample 14 single cell for microglia sequenced with nextseq

description:
Library name: samp14_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: MSC, Passage 3, 2kPa substrate, RNA-Seq, rep2

description: Library name: P3_2-R2


description:
Library name: Sample 31
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7-/-, clone B1, replication 1

value: iPSC-derived excitatory neurons


title: JH1O_H2AX_KO_JH1bait_1

description:
Library name: Sample 43
JH1 bait\, H2AX knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: Sample 12 single cell for microglia sequenced with nextseq

description:
Library name: samp12_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: JH1O_ATMi_JH1bait_1

description:
Library name: Sample 40
JH1 bait\, ATMi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 10 single cell for microglia sequenced with nextseq

description:
Library name: samp10_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: MSC, Passage 3, 2kPa substrate, RNA-Seq, rep1

description: Library name: P3_2-R1


description:
Library name: Sample 30
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/-, clone D5, replication 3

value: NGN2-induced differentiation


title: JH1O_DMSO_JH1bait_3

description:
Library name: Sample 39
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with DMSO on the second day


title: Sample 9 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s9_SingleNuc_nextseq
Single nucleus sequencing of hippocampus

value: Hippocampus

value: Mixed


title: Sample 8 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s8_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: Sample 5 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s5_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: JH1O_DMSO_JH1bait_2

description:
Library name: Sample 38
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 29
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/-, clone D5, replication 2

value: batch 1


title: MSC, Passage 1, 100kPa substrate , RNA-Seq, rep1

description: Library name: P1_100-R1

value: 1 week/passage


description:
Library name: Sample 28
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/-, clone D5, replication 1


title: MSC, Passage 1, 100kPa substrate , RNA-Seq, rep3

description: Library name: P1_100-R3

value: 100kPa substrate


title: JH1O_DMSO_JH1bait_1

description:
Library name: Sample 37
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 25
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/-, clone A2, replication 1


title: Sample 6 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s6_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: MSC, Passage 1, 2kPa substrate, RNA-Seq, rep3

description: Library name: P1_2-R3

value: 2kPa substrate


description:
Library name: Sample 26
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/-, clone A2, replication 2

value: Day 42


title: JH1O_53BP1_KO_53BP1_JH1bait_2

description:
Library name: Sample 35
JH1 bait\, PMX-53BP1-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_53BP1_Flag retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: JH1O_53BP1_KO_53BP1_JH1bait_1

description:
Library name: Sample 34
JH1 bait\, PMX-53BP1-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_KO_53BP1_JH1bait_3

description:
Library name: Sample 36
JH1 bait\, PMX-53BP1-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 7 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s7_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: MSC, Passage 1, 2kPa substrate, RNA-Seq, rep1

description: Library name: P1_2-R1

value: bone marrow


title: MSC, Passage 1, 2kPa substrate, RNA-Seq, rep2

description: Library name: P1_2-R2

value: mesenchymal stromal cell


description:
Library name: Sample 24
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/+, replication 6

value: WT


title: Sample 4 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s4_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: Sample 3 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s3_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


description:
Library name: Sample 27
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/-, clone A2, replication 3


title: JH1O_53BP1_KO_FFR_JH1bait_3

description:
Library name: Sample 33
JH1 bait\, PMX-FFR-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_FFR_Flag retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: JH1O_53BP1_KO_FFR_JH1bait_2

description:
Library name: Sample 32
JH1 bait\, PMX-FFR-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: MSC, Passage 5, transferred from 100kPa substrate to 2kPa substrate after 3 passages, rep2

description: Library name: P5_100T2_4-R2

data_processing:
Sequence reads were trimmed for adaptor sequences and QC metrics assessed using TrimGalore! and FastQC packages, respectively. Reads with Phred quality scores < 20 were excluded from downstream analysis.
Trimmed reads that passed QC were aligned to the rn7 genome using Bowtie2. Paired-end alignments with a maximum fragment length of <500bp were passed forward. Default parameters were used for all remaining alignment options.
Peaks were called on aligned data using MACS2 with significance cut-off q-value <= 0.05.
To generate ATAC-seq coverage plots, regions stratifying 100bp upstram and downstream of peak summits identified using MACS2 were generated for all samples. Biological replicates were merged into a singular bam file using samtools. The resulting bam file(s) was then converted to bigWig file format using the bedtools and kent-tools packages.
Assembly: rn7
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P1_2 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P1_100 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P3_2 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P3_100 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P5_2 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P5_100 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P5_2T100_4 condition.
Supplementary files format and content: Bigwig file generated after merging bam files for all biological replicates of P5_100T2_4 condition.

extract_protocol:
Cells were trypsinized, collected in a 1.5mL DNA Lobind (Eppendorf) tube, and washed with ice cold ATAC-seq resuspension buffer (ATAC-RSB). After washing cells were lysed with ATAC-RSB containing .005% digitonin, .05% NP-40, and .05% Tween-20. Transposition was performed using TDE1 Tn5 tranposase (Nextera) in TD buffer (Nextera) for 45 minutes on a thermoshaker set to 37C with 1000 RPM mixing. The resulting DNA products were purified using a Qiagen MinElute purification kit.
Samples were double-barcoded using Nextera i7 and i5 indexes (Illumina), amplified on a thermocycler, size selected to exclude fragments >600 bp using the SPRIselect system (Beckman-Coulter) and pooled to a final concentration of 20nM. Proper fragment size distribution was validated prior to sequencing via TapeStation (Agilent) as preliminary quality control (QC) to confirm DNA fragment sizes followed the anticipated pattern of nucleosomal periodicity.

value: 100kPa→2kPa substrate

value: 5 weeks/passages


title: JH1O_53BP1_KO_FFR_JH1bait_1

description:
Library name: Sample 31
JH1 bait\, PMX-FFR-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 22
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/+, replication 4

value: iPSC-derived excitatory neurons

value: NGN2-induced differentiation


description:
Library name: Sample 23
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/+, replication 5


title: MSC, Passage 5, transferred from 2kPa substrate to 100kPa substrate after 3 passages, rep2

description: Library name: P5_2T100_4-R2

value: 2kPa→100kPa substrate


title: Sample 2 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s2_SingleNuc_nextseq
Single nucleus sequencing of hippocampus

value: Hippocampus

value: Mixed


title: JH1O_53BP1_KO_delC3_JH1bait_3

description:
Library name: Sample 30
JH1 bait\, PMX-delC3-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_delC3_Flag retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


description:
Library name: Sample 21
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/+, replication 3

value: batch 1


title: Sample 23 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s23_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: JH1O_53BP1_KO_delC3_JH1bait_1

description:
Library name: Sample 28
JH1 bait\, PMX-delC3-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 5, transferred from 100kPa substrate to 2kPa substrate after 3 passages, rep1

description: Library name: P5_100T2_4-R1


title: JH1O_53BP1_KO_delC3_JH1bait_2

description:
Library name: Sample 29
JH1 bait\, PMX-delC3-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 5, 100kPa substrate, rep2

description: Library name: P5_100-R2

value: 100kPa substrate


title: Sample 22 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s22_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


description:
Library name: Sample 20
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/+, replication 2

value: Day 42


title: Sample 21 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s21_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: MSC, Passage 5, 100kPa substrate, rep1

description: Library name: P5_100-R1


description:
Library name: Sample 19
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 42, XPO7+/+, replication 1


title: Sample 24 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s24_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


description:
Library name: Sample 18
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7-/-, clone E12, replication 3

value: Day 28


title: Sample 20 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s20_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: Sample 1 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s1_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: MSC, Passage 5, 2kPa substrate, rep2

description: Library name: P5_2-R2

value: bone marrow

value: 2kPa substrate


title: JH1O_53BP1_KO_delC2_JH1bait_3

description:
Library name: Sample 27
JH1 bait\, PMX-delC2-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_delC2_Flag retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: JH1O_53BP1_KO_delC2_JH1bait_2

description:
Library name: Sample 26
JH1 bait\, PMX-delC2-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 5, 2kPa substrate, rep1

description: Library name: P5_2-R1

value: mesenchymal stromal cell


title: JH1O_53BP1_KO_delC2_JH1bait_1

description:
Library name: Sample 25
JH1 bait\, PMX-delC2-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


description:
Library name: Sample 17
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7-/-, clone E12, replication 2


title: MSC, Passage 5, transferred from 2kPa substrate to 100kPa substrate after 3 passages, rep1

description: Library name: P5_2T100_4-R1


title: Sample 19 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s19_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: MSC, Passage 1, 100kPa substrate , RNA-Seq, rep2

description: Library name: P1_100-R2

value: 1 week/passage


description:
Library name: Sample 15
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7-/-, clone B1, replication 3


title: MSC, Passage 3, 100kPa substrate, rep2

description: Library name: P3_100-R2

value: 3 weeks/passages


title: Sample 18 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s18_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


description:
Library name: Sample 16
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7-/-, clone E12, replication 1

value: iPSC-derived excitatory neurons


title: JH1O_53BP1_KO_delC1_JH1bait_2

description:
Library name: Sample 23
JH1 bait\, PMX-delC1-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_delC1_Flag retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


description:
Library name: Sample 13
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7-/-, clone B1, replication 1

value: NGN2-induced differentiation


title: JH1O_53BP1_KO_delC1_JH1bait_1

description:
Library name: Sample 22
JH1 bait\, PMX-delC1-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MSC, Passage 3, 100kPa substrate, rep1

description: Library name: P3_100-R1


description:
Library name: Sample 14
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7-/-, clone B1, replication 2


title: MSC, Passage 3, 2kPa substrate, rep2

description: Library name: P3_2-R2


title: JH1O_53BP1_KO_delC1_JH1bait_3

description:
Library name: Sample 24
JH1 bait\, PMX-delC1-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_delC1_Flagretrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


description:
Library name: Sample 11
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/-, clone D5, replication 2


title: Sample 14 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s14_SingleNuc_nextseq
Single nucleus sequencing of hippocampus

value: Hippocampus

value: Mixed


description:
Library name: Sample 12
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/-, clone D5, replication 3

value: batch 1


title: MSC, Passage 1, 100kPa substrate , rep1

description: Library name: P1_100-R1

value: 100kPa substrate


title: JH1O_53BP1_KO_vector_JH1bait_3

description:
Library name: Sample 21
JH1 bait\, PMX-vector-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX_vector retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: Sample 15 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s15_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: JH1O_53BP1_KO_vector_JH1bait_2

description:
Library name: Sample 20
JH1 bait\, PMX-vector-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 10
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/-, clone D5, replication 1

value: Day 28


title: Sample 17 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s17_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: Sample 13 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s13_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: MSC, Passage 1, 100kPa substrate , rep2

description: Library name: P1_100-R2

value: bone marrow


title: JH1O_53BP1_KO_vector_JH1bait_1

description:
Library name: Sample 19
JH1 bait\, PMX-vector-Flag infected\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: PMX-vector retrovirally complemented\, RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: JH1O_53BP1_KO_JH1bait_3

description:
Library name: Sample 18
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: MSC, Passage 1, 2kPa substrate, rep2

description: Library name: P1_2-R2

value: mesenchymal stromal cell

value: 2kPa substrate


title: MSC, Passage 3, 2kPa substrate, rep1

description: Library name: P3_2-R1


description:
Library name: Sample 9
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/-, clone A2, replication 3


title: MSC, Passage 1, 2kPa substrate, rep1

description: Library name: P1_2-R1

value: 1 week/passage


title: Sample 16 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s16_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: JH1O_53BP1_KO_JH1bait_1

description:
Library name: Sample 16
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: Sample 11 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s11_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


title: Sample 12 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s12_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


description:
Library name: Sample 8
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/-, clone A2, replication 2

value: iPSC-derived excitatory neurons


title: JH1O_53BP1_KO_JH1bait_2

description:
Library name: Sample 17
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 10 single nuclei from hippocampus sequenced with nextseq

description:
Library name: s10_SingleNuc_nextseq
Single nucleus sequencing of hippocampus


description:
Library name: Sample 7
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/-, clone A2, replication 1


description:
Library name: Sample 5
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/+, replication 5

value: WT


title: JH1O_JH1bait_2

description:
Library name: Sample 14
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 6
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/+, replication 6

value: NGN2-induced differentiation


title: Rat_Kidney_Sham_M_DSP-1010707202201-E-C03

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

description:
Library name: DSP-1010707202201-E-C03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

data_processing:
Raw sequencing data were processed to generate FASTQ files using GeoMx NGS Pipeline.
A gene was called detected if the signal to noise (SNR) was ≥ 4, where the limit of quantitation (LoQ) is defined as GeoMean(NegProbes)*GeoSD(NegProbes)2.
Gene counts were normalized by Q3 normalization after the removal of genes below the detection threshold.
Assembly: GRCh38 / hg38
Supplementary files format and content: target_NanoString_Q3Norm.tsv: gene expression count table with Q3 normalization in .tsv format
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
4 um Formalin-fixed paraffin-embedded rat kidney sections were used.
132 specific ROIs within 3 rats per condition (Sham, HS, RM, RM-HS) were selected for spatial transcriptomic profiling usins DSP GeoMX Nanostring technology. We manually selected regions of interest (ROIs) from four kidney areas: glomeruli (G), cortex (C), corticomedullary junction (CMJ), and medulla (M). Slides were incubated with GeoMx Mouse WTA (Nanostring) assay probe cocktail overnight. The slides were applied with morphology markers incubation before loading onto GeoMx machine.
Library preparations were carried out according to the GeoMx NGS Readout Library Prep Manual (MAN-10117; NanoString). Libraries were sequenced on an Illumina NovaSeq6000 according to the manufacturer’s instructions.

value: Kidney

tag: group

value: Sham

tag: region

value: M


title: Rat_Kidney_Sham_M_DSP-1010707202201-E-C04

description:
Library name: DSP-1010707202201-E-C04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: mCAF1 H3K27ac input

city: Santander

first: Fernando

last: Calvo

state: Cantabria

address: C. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: mCAF1 (INPUT)

data_processing:
Raw sequencing files processed by the Illumina NextSeq500 sequencer were obtained in “FASTQ” format. Raw data was pre-processed to perform quality check and removal of contaminants. The raw sequencing files were then aligned using the mouse reference genome 38 (GRCm38) as reference. MACS2 was used for peak calling, and Bedtools for overlap and subsetting analysis. Tracks were visualized using the UCSC Genome Browser (https://genome.ucsc.edu/), focusing in the indicated areas.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig for each sample

source_name: mammary gland

growth_protocol: Established hpv-E6 immortalized murine fibroblasts from FVB/n normal mammary glands (mNF1) and MMTV-PyMT mammary carcinoma (mCAF1) were maintained in high glucose DMEM supplemented with 10% Fetal Bovine Serum (FBS), 1% GlutaMax and Pen/Strep antibiotics in a standard humidified 5% CO2 incubator at 37C.

extract_protocol:
Briefly, 7-10 × 106 cells at subconfluency were fixed in 1% formaldehyde, washed, lysed and sonicated using the Bioruptor Pico sonication device (Diagenode; B01060001) using 10 cycles (30 sec on; 30 sec off) at maximum intensity. Purified chromatin was then separated for: (i) immunoprecipitation using Dynabeads Protein G (Life Technologies: 10003D) coated with 10 µg of Rabbit anti-Histone H3 acetyl K27 antibody (Abcam, ab4729) per ChIP experiment; (ii) non-immunoprecipitated chromatin, used as Input control; and (iii) assessment of sonication efficiencies using a 1% agarose gel. ChIP DNA was washed, eluted and treated with 2.7 μL of 1 mg/mL RibonucleaseA (RNaseA) for 30 min at 37 °C and subsequently incubated with 1.3 μL of 20 mg/mL proteinase K (Invitrogen) for 1 h at 55 °C. Then DNA extraction was performed using SPRI magnetic beads (Beckman Coulter, B23318). After elution in TE buffer, DNA was quantified using Qubit (ThermoFisher Scientific; Qubit 3.0 Fluorometer; #Q33216) high sensitivity assay (ThermoFisher Scientific; #33216)
Prior to sequencing, ChIP samples were library prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEBNext Ultra II DNA library prep kit for Illumina, #E7770, NEBNext Multiplex Oligos for Illumina, #E7335L). Adaptor ligated DNA was size selected with SPRI magnetic beads (Beckman Coulter, B23318) for the Illumina sequencer (#NextSeq500). After library preparation, we performed qPCR, high sensitivity DNA quantification and size selection measurement (Agilent Bioanalyzer 2100 system + High sensitivity DNA measurement assay; 5067–4626) before sending samples for sequencing.

treatment_protocol: Cells were seeded at 60% confluency in regular tissue culture dishes and cultured for 2 days in normal culture conditions before analysis

value: mammary gland

value: cancer-associated fibroblasts

tag: chip antibody


description:
Library name: Sample 3
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/+, replication 3

value: Day 28

value: batch 1


title: Rat_Kidney_Sham_M_DSP-1008220000001-C-F04

description:
Library name: DSP-1008220000001-C-F04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 53BP1_KO_JH4RSSbait_3

description:
Library name: Sample 12
JH4-RSS bait\, 53BP1 knockout\, Emu-Bcl2\, RAG1 deficient

value: RAG1 retrovirally complemented\, 3 uM STI-571 treated for 4 days


description:
Library name: Sample 2
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/+, replication 2


title: JH1O_JH1bait_3

description:
Library name: Sample 15
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: Rat_Kidney_Sham_M_DSP-1008220000001-C-F03

description:
Library name: DSP-1008220000001-C-F03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: mCAF1 H3K27ac ChIP-Seq

description: Library name: mCAF1 (H3K27ac ChIP)

value: Rabbit anti-Histone H3 acetyl K27 antibody (Abcam, ab4729)


description:
Library name: Sample 1
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 28, XPO7+/+, replication 1


title: TM4 cells, Ang overexpression, replicate 2

city: Seoul

first: Yoon Jung

last: Park

address: 52 Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

description: Library name: TM4_AngOE_2

library_source: other

data_processing:
Data quality was assessed using FastQC (v0.12.0). Sequence reads were trimmed for TruSeq small RNA 3’ adapter sequences and low-quality sequence using Trimmomatic (v0.40). Trimmed sequence reads were annotated using the SPORTS1.1 annotation pipeline with one mismatch and default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (output file from SPORTS1.1)

molecule: other

growth_protocol: TM4 Sertoli cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using TRIzol reagent and 1 µg of RNA was used for sequencing library construction. Mature sperm were isolated from epididymis and three individual sperm samples were pooled to generate one biological replicate.
RNA libraries for smallRNA-seq were prepared using TruSeq Small RNA Library Prep Kit following manufacture’s protocols.

treatment_protocol: TM4 cells were treated with Compound C at a concentration of 10 µM for 12 hours. For Ang overexpression, the full-length Ang coding sequence was cloned using the Gateway system and subsequently overexpressed. Mice were fed the control diet (16% kcal from fat, AIN-93G) for 7 weeks starting at 4 weeks of age. Mice were fed the high-fat diet (69% kcal from fat, D12492) for 7 weeks starting at 4 weeks of age.

value: mouse Sertoli cell

value: Angiogenin overexpression


title: Rat_Kidney_Sham_M_DSP-1010707202201-E-C02

description:
Library name: DSP-1010707202201-E-C02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 53BP1_KO_JH4RSSbait_1

description:
Library name: Sample 10
JH4-RSS bait\, 53BP1 knockout\, Emu-Bcl2\, RAG1 deficient

value: v-Abl transformed pro-B cell line


title: JH1O_JH1bait_1

description:
Library name: Sample 13
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Rat_Kidney_Sham_M_DSP-1008220000001-C-C06

description:
Library name: DSP-1008220000001-C-C06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: WT_JH4RSSbait_3

description:
Library name: Sample 9
JH4-RSS bait\, Emu-Bcl2\, RAG1 deficient

value: Emu-Bcl2\, RAG1 deficient


title: mNF1 H3K27ac ChIP-Seq

description: Library name: mNF1 (H3K27ac ChIP)

value: normal fibroblasts


title: Rat_Kidney_Sham_M_DSP-1008220000001-C-F02

description:
Library name: DSP-1008220000001-C-F02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: TM4 cells, Ang overexpression, replicate 1

description: Library name: TM4_AngOE_1


title: WT_JH4RSSbait_1

description:
Library name: Sample 7
JH4-RSS bait\, Emu-Bcl2\, RAG1 deficient


title: Ribo Isogenic3

city: Belfast

first: Sarah

last: Maguire

address: 97 Lisburn Road

department: PGJCCR

country: United Kingdom

institute: Queen's University Belfast

description: Library name: Isogenic3

data_processing:
Raw Ribo-seq reads were adapter-trimmed and size-selected to retain fragments 28-32 nt in length. Reads were aligned to the human transcriptome (GRCh38) using STAR (v2.7.10b). P-site positions were computed using riboWaltz (v2.0) with automatic offset detection, confirming 3-nt periodicity across coding regions.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes DESeq2 normalised counts values for each Sample
Library strategy: Ribo-Seq

source_name: midbrain organoid

growth_protocol: iPSC lines were maintained at 37°C with 5% CO₂ in mTeSR Plus (STEMCELL Technologies, #05825) on Matrigel®-coated plates (Corning, #354277) and passaged using 0.5 mM EDTA (Thermo Fisher Scientific, #15575020). For generation of human midbrain organoids (hMOs), iPSCs were used only after at least two passages following thawing and were not passaged more than ten times. hMOs were generated as previously described14. Briefly, 10,000 cells from a single-cell suspension of iPSCs were seeded into each well of a Nunclon™ Sphera™ 96-well, U-bottom, Sphera-treated microplate (Thermo Scientific™, #174925) containing neuronal induction medium [DMEM/F12:Neurobasal (1:1) (Gibco, #21103049), supplemented with 1:100 N2 (Thermo Fisher Scientific, #17502048), 1:50 B27 without vitamin A (Thermo Fisher Scientific, #12587010), 1% GlutaMAX (Thermo Fisher Scientific, #35050061), 1% MEM Non-Essential Amino Acids (Thermo Fisher Scientific, #11140-050), and 0.1% β-mercaptoethanol (Gibco, #21985-023), along with 1 μg/mL heparin (Sigma-Aldrich, #H3149-10KU), 10 μM SB431542 (Selleck Chemicals, #S1067), 200 ng/mL Noggin (ImmunoTools, #11344834-rh), 0.8 μM CHIR99021 (Cayman, #13122), and 10 μM ROCK inhibitor Y27632 (Cayman, #129830-38-2)]. Plates were centrifuged for 3 min at 1200 rpm to aggregate the cells. After 48 h, embryoid bodies (EBs) were formed, and the medium was replaced with fresh neuronal induction medium lacking ROCK inhibitor. Two days later, the medium was replaced with midbrain patterning medium [neuronal induction medium supplemented with 200 ng/mL SHH-C25II (ImmunoTools, #11344074) and 100 ng/mL FGF8 (ImmunoTools, #11344834)] to promote midbrain identity. After 3 additional days, EBs were embedded in reduced growth factor Matrigel®GFR (Corning, #354230) and incubated for 24 h in tissue induction medium [neurobasal medium supplemented with 1:100 N2, 1:50 B27 without vitamin A, 1% GlutaMAX, 1% MEM Non-Essential Amino Acids, 0.1% β-mercaptoethanol, 2.5 μg/mL Insulin (Capricorn Scientific, #INS-K), 200 ng/mL laminin (Sigma-Aldrich, #L2020), 100 ng/mL SHH-C25II, and 100 ng/mL FGF8]. The following day, embedded hMOs were transferred to six-well ultra-low attachment plates containing final differentiation medium [neurobasal medium supplemented with 1:100 N2, 1:50 B27 without vitamin A, 1% GlutaMAX, 1% MEM Non-Essential Amino Acids, 0.1% β-mercaptoethanol, 10 ng/mL BDNF (ImmunoTools, #11343375), 10 ng/mL GDNF (ImmunoTools, #11343793), 100 μM ascorbic acid (Sigma-Aldrich, #A8960-5g), and 125 μM db-cAMP (Santa Cruz Biotechnology, #sc-201567A)] and cultured on an orbital shaker (Heathrow Scientific, #5003396). Full media exchanges were performed 3 times per week. For quality control, mycoplasma testing was performed monthly on both iPSCs and hMOs to confirm the absence of contamination.

extract_protocol:
Organoids were incubated in maturation medium supplemented with 10 μg/mL cycloheximide (CHX) for 5 min, washed twice with cold DPBS containing 20 μg/mL CHX, and snap-frozen in liquid nitrogen. Ten frozen organoids per sample were pooled and pulverized under liquid nitrogen using a mortar and pestle. The powder was collected in a 1.5 mL tube and resuspended in 400 μL Tissue Lysis Buffer (Immagina, #RL001-02) supplemented with 10% sodium deoxycholate (Thermo Scientific, #89904), 1 U/μl DNase I (Invitrogen, #AM2222), and 40 U/μl RiboLock RNase Inhibitor (Thermo Fisher Scientific, #EO0381), and centrifuged according to the manufacturer’s protocol. The absorbance units (AU) of the samples were measured using a NanoDrop spectrophotometer at 260 nm. Ribosome-protected fragment pulldown. High Affinity ribosome beads (hiRB; Immagina, #GF001-04) were prepared for pulldown according to the functionalization protocol. Tissue lysates were subjected to nuclease digestion during the bead functionalization step. A fraction of each lysate was retained as an internal mRNA control (total mRNA). The digested lysates were incubated with functionalized beads for 70 min to allow ribosome binding. Ribosome-protected fragments (RPFs; length: 28–32 nt) were then purified using RNA Clean & Concentrator-5 (Zymo Research, #R1015).
Library preparation. RPF library preparation was carried out according to the manufacturer’s instructions and included the following steps: A. 5′ phosphorylation, B. Adapter ligation, C. Circularization, D. Reverse transcription, E. PCR amplification, F. PCR amplification 2, G. Library quality check, H. Sequencing. Sequencing was performed as a service by Immagina Biotechnology (Italy) on a NovaSeq 6000 instrument (Illumina).

treatment_protocol: .Organoids were incubated in maturation  medium supplemented with 10 μg/mL cycloheximide (CHX) for 5 min

value: midbrain organoid

value: SNCA Isogenic (AST23-2KO-8B P11MT)

value: hiPSCs

value: isogenic

value: cycloheximide

value: batch 2


title: Ribo Isogenic2

description: Library name: Isogenic2


title: TM4 cells, CC treatment, replicate 2

description: Library name: TM4_CC_2

value: Compound C treatment


title: Rat_Kidney_Sham_M_DSP-1008220000001-C-C05

description:
Library name: DSP-1008220000001-C-C05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: Sham

value: M


title: 53BP1_KO_JH1-4bait_3

description:
Library name: Sample 6
JH1-4 bait\, 53BP1 knockout\, Emu-Bcl2\, RAG1 deficient

value: RAG1 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: mNF1 H3K27ac input

description: Library name: mNF1 (INPUT)

value: mammary gland


title: Ribo Isogenic1

description: Library name: Isogenic1


title: TM4 cells, CC treatment, replicate 1

description: Library name: TM4_CC_1

value: mouse Sertoli cell


title: Rat_Kidney_Sham_M_DSP-1008220000001-C-C07

description:
Library name: DSP-1008220000001-C-C07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_Sham_G_DSP-1010707202201-E-C12

description:
Library name: DSP-1010707202201-E-C12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: G


title: Rat_Kidney_Sham_G_DSP-1010707202201-E-D01

description:
Library name: DSP-1010707202201-E-D01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: TM4 cells, control, replicate 2

description: Library name: TM4_Ctrl_2

value: Control


title: Rat_Kidney_Sham_G_DSP-1010707202201-E-C11

description:
Library name: DSP-1010707202201-E-C11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 53BP1_KO_JH1-4bait_2

description:
Library name: Sample 5
JH1-4 bait\, 53BP1 knockout\, Emu-Bcl2\, RAG1 deficient

value: v-Abl transformed pro-B cell line


title: WT_JH1-4bait_2

description:
Library name: Sample 2
JH1-4 bait\, Emu-Bcl2\, RAG1 deficient

value: Emu-Bcl2\, RAG1 deficient


title: Sperm from HFD, replicate 3

description: Library name: Sperm_HFD_3

source_name: sperm

value: sperm

value: High fat diet


title: WT_JH1-4bait_1

description:
Library name: Sample 1
JH1-4 bait\, Emu-Bcl2\, RAG1 deficient


title: Ribo Triplication2

description: Library name: Triplication2

value: midbrain organoid

value: SNCA Triplication (AST23 P35+P7 MT)

value: hiPSCs

value: triplication


title: TM4 cells, control, replicate 1

description: Library name: TM4_Ctrl_1


title: 53BP1_KO_JH1-4bait_1

description:
Library name: Sample 4
JH1-4 bait\, 53BP1 knockout\, Emu-Bcl2\, RAG1 deficient


title: Ribo Triplication3

description: Library name: Triplication3

value: cycloheximide

value: batch 2


title: RiboTriplication1

description: Library name: Triplication1


title: Rat_Kidney_Sham_G_DSP-1008220000001-C-G01

description:
Library name: DSP-1008220000001-C-G01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: Sham


title: Sperm from HFD, replicate 2

description: Library name: Sperm_HFD_2


title: Rat_Kidney_Sham_G_DSP-1008220000001-C-F12

description:
Library name: DSP-1008220000001-C-F12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Sperm from HFD, replicate 1

description: Library name: Sperm_HFD_1


title: WT_JH1-4bait_3

description:
Library name: Sample 3
JH1-4 bait\, Emu-Bcl2\, RAG1 deficient

value: RAG1 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: RNA Triplication3

description: Library name: Triplication3

data_processing:
Raw RNA-seq reads were trimmed using Trimmomatic v0.36 to remove adapters and low-quality bases. Trimmed reads were aligned to the human reference genome (GRCh38 , ENSEMBL) using STAR v2.5.2b. Gene-level counts were generated with featureCounts (Subread v1.5.2), including only uniquely mapped reads to exonic regions.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes DESeq2 normalised counts values for each Sample

extract_protocol:
D100 organoids were transferred from culture plates to 1.5 mL tubes and briefly washed in ice-cold DPBS. For each biological replicate, 3 organoids were pooled in the same tube. After complete removal of DPBS, organoids were homogenized using QIAshredder homogenizers (Qiagen, #79656), and total RNA was extracted using the RNeasy Micro Kit (Qiagen, #74004) according to the manufacturer’s instructions.
Library preparation and RNA sequencing were performed as a service by GENEWIZ/AZENTA and sequenced on a NovaSeq 6000 instrument (Illumina).


title: RNA Triplication1

description: Library name: Triplication1


title: RNA Isogenic3

description: Library name: Isogenic3

value: SNCA Isogenic (AST23-2KO-8B P11MT)

value: isogenic


title: Rat_Kidney_Sham_G_DSP-1008220000001-C-D04

description:
Library name: DSP-1008220000001-C-D04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: G


title: iILC2_Stat4ko_4

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

description: Library name: Sample_8

data_processing:
The resulting FASTQ files were preprocessed with Trimmomatic (v0.39) for adapter trimming and low-quality filtering of the reads (24695404). Filtered sequence reads were aligned to reference GRCm38 mouse transcriptome (mm10) with HISAT2 aligner (v2.2.1) and raw counts were obtained with FeatureCounts (subread v2.0.1) . GENCODE Gene Set version M27 was used for gene annotation.
Assembly: mm10
Supplementary files format and content: comma-delimited file containing raw counts of each sample

source_name: Lung

extract_protocol:
30-50,000 ILC2 were FACS-sorted as L/D-CD3ε- CD19-NK1.1, KLRG1+ cells from the lungs. RNA was isolated by single cell purification kit (Norgen, #51800) using RNase-Free DNase (Norgen #25710).
Sequencing libraries were generated using SMARTer® Stranded Total RNA-seq Kit v2 (Takara Bio).

treatment_protocol: Rag2-/- and Rag2-/-Stat4-/- mice were IL-25-treated for 3 days.

value: Lung

value: Primary

value: 3 days with IL-25


title: Rat_Kidney_Sham_G_DSP-1008220000001-C-F11

description:
Library name: DSP-1008220000001-C-F11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_Sham_G_DSP-1008220000001-C-D02

description:
Library name: DSP-1008220000001-C-D02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: RNA Isogenic2

description: Library name: Isogenic2


title: RNA Isogenic1

description: Library name: Isogenic1


title: iILC2_Stat4ko_1

description: Library name: Sample_5


title: Sperm from CD, replicate 3

description: Library name: Sperm_CD_3

value: sperm

value: Control diet


title: RNA Triplication2

description: Library name: Triplication2

value: midbrain organoid


title: mKPC-GB-Luc-Rep3

city: Birmingham

first: Sujith

last: Sarvesh

state: Alabama

address: 1824 6th Ave S

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: Sample 6

data_processing:
nf-core/rnaSeq pipeline
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab -separated values files

source_name: mKPC-GB-Luc

growth_protocol: GEM-KPC mice (LSL-KrasG12D/+; LSL-Trp53 R172H/+; Pdx-1-Cre) were obtained from Jackson Laboratory (Bar Harbor, Maine). These mice were created by mating LSL-KrasG12D/+ with LSL-Trp53R172H/+ and then breeding the resulting heterozygotes with Pdx-1-Cre. GEM-KPC mouse treatments began at 14 weeks of age. Experimental details were described and depicted in Table 1 and Figure 4A. Initially, they were treated with ProAgio (10mg/Kg; IP) for 10 consecutive doses, trailed by 10 doses every other day. Gemcitabine (50mg/Kg; IP) treatment was initiated after 5 doses of ProAgio and administered once every 2 days.

extract_protocol:
The TRIzol procedure was used to isolate total RNA according to the manufacturer's instructions. RNA was purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany), and mRNA was extracted from 500 ng of purified total RNA using oligo (dT) beads. RNA sequencing was performed on six samples, including two groups (KPC-Luc and mKPC-GB-Luc). Each group has three biological replicates.
admera Health protocol

treatment_protocol: Described in previous section

value: mKPC-GB-Luc

value: Ductal Epithelialcell


title: Rat_Kidney_Sham_G_DSP-1008220000001-C-D03

description:
Library name: DSP-1008220000001-C-D03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Sperm from CD, replicate 2

description: Library name: Sperm_CD_2


title: iILC2_Stat4ko_2

description: Library name: Sample_6


title: Rat_Kidney_Sham_CMJ_DSP-1010707202201-E-C07

description:
Library name: DSP-1010707202201-E-C07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: CMJ


title: MDA-MB231, R1

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

description: Library name: APE1, Sample 8_ChIP_APE1

data_processing:
RNAseq Reads were aligned and mapped to reference genome using STAR
Peaks from bigwig files were visualized using IGV
TPM values were calculated using DESeq2
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample and Deseqresults file for RNAseq
Supplementary files format and content: bigwig for ChIP data

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104). RNA concentration and purity were measured using a NanoDrop spectrophotometer (Thermo Fisher). Samples were subjected to quality control and library preparation at the UNMC Sequencing Core Facility, followed by next-generation sequencing.

treatment_protocol: Coding sequences of wild-type APE1 and its mutants were cloned into the doxycycline-inducible pCW57 lentiviral vector (Addgene #80921). APE1-knockout TNBC cells were transduced with the lentiviruses and selected with 40 μg/mL blasticidin (AG Scientific). Doxycycline (TaKaRa) was used to induce APE1 expression.

value: Human Breast Cancer Cell Line


title: Sperm from CD, replicate 1

description: Library name: Sperm_CD_1


title: iILC2_WT_4

description: Library name: Sample_4


title: Mulitplexed(Sham,ProAgio,Gemcitabine,Gem_ProAgio)

description:
Library name: Sample 1
10x Genomics

data_processing:
Cell Ranger version 9.0.1 from 10xGenomicas pipeline for scRNAseq
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab -separated values files and matrix files

source_name: Pancreatic Tumor

extract_protocol:
admera Health protocol
admera Health protocol

value: Pancreatic Tumor

value: GEMM-KPC


title: Rat_Kidney_Sham_CMJ_DSP-1010707202201-E-C06

description:
Library name: DSP-1010707202201-E-C06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: Sham


title: MDA-MB-231, Input

description: Library name: APE1, Sample 7_ChIP_input


title: mKPC-GB-Luc-Rep2

description: Library name: Sample 5


title: iILC2_WT_2

description: Library name: Sample_2


title: Rat_Kidney_Sham_CMJ_DSP-1010707202201-E-C05

description:
Library name: DSP-1010707202201-E-C05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: iILC2_WT_3

description: Library name: Sample_3


title: mKPC-GB-Luc-Rep1

description: Library name: Sample 4


title: Rat_Kidney_Sham_CMJ_DSP-1008220000001-C-F07

description:
Library name: DSP-1008220000001-C-F07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: MDMA_parent3

description: Library name: Sample 5


title: Rat_Kidney_Sham_CMJ_DSP-1008220000001-C-F06

description:
Library name: DSP-1008220000001-C-F06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: pKPC-Luc-Rep3

description: Library name: Sample 3

source_name: pKPC-Luc

value: pKPC-Luc


title: MDMA_parent1

description: Library name: Sample 3


title: low_2_1.fq.gz

city: Shanghai

first: Juanjuan

last: Shi

address: 160 Pujian Rd Shanghai 200127 P. R. China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

description: Library name: sorted KPC1199 ly6D low expression-2 cells

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.RNA-seq reads were aligned to the mm9genomes by HISAT2 with default parameters. All unmapped reads were removed. Read counts were calculated by featureCounts using uniquely mapped reads, and differentially expressed genes were identified by DESeq2 with a cut-off of more than 1.5-fold change and a P value of less than 0.05.
Assembly: mm9
Supplementary files format and content: gene expression matrix,excel sheet

source_name: KPC1199 cells sorted from orthotopical pancreatic cancer tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)


title: pKPC-Luc-Rep2

description: Library name: Sample 2


title: MDMA_parent2

description: Library name: Sample 4


title: Rat_Kidney_Sham_CMJ_DSP-1008220000001-C-F05

description:
Library name: DSP-1008220000001-C-F05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: low_1_1.fq.gz

description: Library name: sorted KPC1199 ly6D low expression-1 cells

value: KPC1199 cells sorted from orthotopical pancreatic cancer tissue


title: hi_2_1.fq.gz

description: Library name: sorted KPC1199 ly6D high expression-2 cells


title: MDMA_KD2

description: Library name: Sample 2


title: MDMA_KD1

description: Library name: Sample 1


title: Rat_Kidney_Sham_CMJ_DSP-1008220000001-C-C10

description:
Library name: DSP-1008220000001-C-C10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: iILC2_WT_1

description: Library name: Sample_1


title: pKPC-Luc-Rep1

description: Library name: Sample 1


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep16

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: 116 Manning Drive, CB# 7250 Room 7202A, Mary Ellen Jones Building

department: Genetics

institute: UNC Chapel Hill

description:
Library name: RNA Replicate 16 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna16

data_processing:
Adapter sequences were trimmed using cutadapt (v4.1) using default parameters. Trimmed sequences were then converted to reverse complement DNA sequences. We extracted only sequences with 20 bp length and perfectly matched to the barcode information in the barcode-variant table which consists of the unique barcode-variant pairs. In the original paper, we excluded replicates 12 and 13 due to low correlations to other replicates.
Supplementary files format and content: barcode read count matrices contain DNA and RNA barcode read counts from each replicate. (CSV format)
Supplementary files format and content: barcode variant map contains barcode assinged to variant. Since this is random barcode, some barcode found in multiple variants, in such case, unique barcode-variant pairs might need to be extracted for the downstream analysis. (tsv format)

source_name: primary human neural progenitors

growth_protocol: Donor number 88 was used for these experiments and is biologically male. 6-well plates were coated with Poly-L-Ornithine (10 μg/ml; Sigma-Aldrich, cat#P3655-100MG) and Laminin (10ug/mL, Corning, cat#354232). After coating, phNPCs were plated at a concentration of 400,000 cells per well. The cells were plated and fed with growth factors as described (McAfee, J. C. et al. ,2023). 24 hours after plating, the cells were half fed with the media and growth factors described(McAfee, J. C. et al. ,2023). 48 hours after plating, the cells were half-fed with the media and growth factors as described22, and with nucleic acid transfection enhancer (NATE) (1:100 final dilution; InvivoGen, cat#lyec-nate).

extract_protocol:
At exactly 48 hours after CHIR or vehicle treatment, RNA and DNA was extracted from the cells using the Quick-DNA/RNA Miniprep Plus Kit (Zymo, cat#D7003), with 600 µL of Shield Buffer and 600 µL of Lysis Buffer per well.
Extracted RNA was reverse-transcribed into cDNA using SuperScript IV Reverse Transcriptase (Invitrogen, cat. no. 18090050) and a primer designed to bind downstream of the barcodes (Lib_Hand_RT). The resulting cDNA was then amplified with Lib_Hand and Lib_seq_Luc_R primers, utilizing NEBNext 2X Q5 Hifi HS Mastermix, and then purified using the Zymo DNA Clean and Concentrator kit-25 (Zymo, cat. no. D4033). Additionally, 4 µL of DNA from each well was PCR amplified in four separate PCR reactions using Lib_Hand_RT and Lib_Seq_Luc_R primers with NEBNext 2X Q5 Hifi HS Mastermix, followed by purification with the Zymo Clean and Concentrator kit-25. P5 and P7 adapter sequences and i7 demultiplexing indices were then incorporated into both cDNA and DNA libraries through PCR using P5_seq_Luc_F and P7_Ind_#_Han primers with NEBNext 2X Q5 Hifi HS Mastermix. The final PCR products were purified and size-selected using AMPure XP Beads (Beckman Coulter, cat. no. A63881) at 0.7X and 0.9X ratios to isolate a 273 bp DNA fragment.

treatment_protocol: 30 minutes after feeding, the cells were transfected with PJD_lib_minP_Luc plasmid via Lipofectamine Stem Transfection Reagent (Invitrogen, cat#STEM00001) according to the instructions, using Opti-Mem (Thermo Scientific, cat#31985070), 2.5ug of PJD_lib_minP_Luc plasmid, and 1ug of pUC19 plasmid (Thermo Scientific, cat#SD0061) per single 6-well. Co-transfecting with pUC19 plasmid increased transfection efficiency. 24 hours after transfection, the cells were half fed and then treated either with 7uL of 2.5uM CHIR or 7uL DMSO (vehicle).

value: primary human neural progenitors

value: Stimulation (CHIR)


title: RNA-Seq wild-type rep 3

city: Redwood City

first: Jin

last: Chen

state: CA

address: 2400 Bridge Parkway

department: Institute of Science

institute: Altos Labs

description: Library name: RNA_WT_rep3

data_processing:
For Ribo-Seq, FASTX-trimmer and FASTX-clipper (http://hannonlab.cshl.edu/fastx_toolkit/) were used to trim the reads to 50 bp and remove the linker sequences (AGATCGGAAGAGCACACGTCTGAACTC). Reads corresponding to rRNAs were excluded using Bowtie v1.1.2 (http://bowtie-bio.sourceforge.net/) and the remaining reads were aligned to the GRCm39/mm39 transcriptome using tophat v2.1.1 (https://ccb.jhu.edu/software/tophat/) using flag sets as follow: --b2-very-sensitive --transcriptome-only --no- novel-juncs --max-multihits=64 flags. We then used the plastid cs program (Dunn and Weissman, 2016) to calculate counts per gene and normalized counts per gene (in reads per kilobase per million mapped reads, or RPKM), with counts assigned to the ribosome P-site determined by the plastid psite program. The corresponding RNA-seq data were analyzed similarly, using FASTX-trimmer, -reverse_complement,  and trim the reads to 50 bp, reverse complement, and remove the linker sequence (CTGTAGGCACCATCAAT).
Assembly: GRCm39
Supplementary files format and content: Counts and RPKM table

source_name: Brain tissue

extract_protocol:
RNA was isolated using Trizol LS followed by a cleanup column (Zymo).  RNA content was quantified using a nanodrop and samples were sent for library preparation and sequencing at Novogene.  For Ribo-seq, corticsal samples were digested with Rnase T1 and monosomes were separated on sucrose gradients.  RNA from monosome fractions were then purified and subjected to library preparation.
RNA-Seq libraries were prepared using standard poly(A) mRNA procedures by Novogene.  Ribo-Seq libraries were prepared using the small RNA library preparation kit (NEB) as per the manufacturer's instructions.

value: Brain tissue

value: Wild-type


title: Rat_Kidney_Sham_CMJ_DSP-1008220000001-C-C09

description:
Library name: DSP-1008220000001-C-C09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: iILC2_Stat4ko_3

description: Library name: Sample_7

value: Lung

value: Primary

value: 3 days with IL-25


title: hi_1_1.fq.gz

description: Library name: sorted KPC1199 ly6D high expression-1 cells


title: Rat_Kidney_Sham_CMJ_DSP-1008220000001-C-C08

description:
Library name: DSP-1008220000001-C-C08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep15

description:
Library name: RNA Replicate 15 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna15


title: RNA-Seq wild-type rep 2

description: Library name: RNA_WT_rep2


title: OE_2_1.fq.gz

description: Library name: sorted KPC1199 ly6D overexpression-2 cells


title: RNA-Seq wild-type rep 1

description: Library name: RNA_WT_rep1


title: OE_1_1.fq.gz

description: Library name: sorted KPC1199 ly6D overexpression-1 cells


title: Rat_Kidney_Sham_C_DSP-1010707202201-E-C09

description:
Library name: DSP-1010707202201-E-C09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: C


title: pxpr_2_1.fq.gz

description: Library name: sorted KPC1199 ly6D WT-2 cells


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep13

description:
Library name: RNA Replicate 13 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna13


title: RNA-Seq mutant rep 3

description: Library name: RNA_mutant_rep3

value: Ppp1r15b mutant (ISR on)


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep14

description:
Library name: RNA Replicate 14 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna14


title: Rat_Kidney_Sham_C_DSP-1010707202201-E-C08

description:
Library name: DSP-1010707202201-E-C08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: pxpr_1_1.fq.gz

description: Library name: sorted KPC1199 ly6D WT-1 cells


title: Rat_Kidney_Sham_C_DSP-1010707202201-E-C10

description:
Library name: DSP-1010707202201-E-C10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep12

description:
Library name: RNA Replicate 12 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna12


title: RNA-Seq mutant rep 2

description: Library name: RNA_mutant_rep2


title: RNA-Seq mutant rep 1

description: Library name: RNA_mutant_rep1


title: L1EEL270029_KPC1199m3_5.R1.raw.fastq.gz

description: Library name: KPC1199 ly6D overexpression-5 tissue

source_name: orthotopical pancreatic cancer tissue

value: orthotopical pancreatic cancer tissue


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep11

description:
Library name: RNA Replicate 11 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna11


title: L1EEL270028_KPC1199m3_4.R1.raw.fastq.gz

description: Library name: KPC1199 ly6D overexpression-4 tissue


title: Ribo-Seq wild-type rep 2

description: Library name: RP_WT_rep2

data_processing:
For Ribo-Seq, FASTX-trimmer and FASTX-clipper (http://hannonlab.cshl.edu/fastx_toolkit/) were used to trim the reads to 50 bp and remove the linker sequences (AGATCGGAAGAGCACACGTCTGAACTC). Reads corresponding to rRNAs were excluded using Bowtie v1.1.2 (http://bowtie-bio.sourceforge.net/) and the remaining reads were aligned to the GRCm39/mm39 transcriptome using tophat v2.1.1 (https://ccb.jhu.edu/software/tophat/) using flag sets as follow: --b2-very-sensitive --transcriptome-only --no- novel-juncs --max-multihits=64 flags. We then used the plastid cs program (Dunn and Weissman, 2016) to calculate counts per gene and normalized counts per gene (in reads per kilobase per million mapped reads, or RPKM), with counts assigned to the ribosome P-site determined by the plastid psite program. The corresponding RNA-seq data were analyzed similarly, using FASTX-trimmer, -reverse_complement,  and trim the reads to 50 bp, reverse complement, and remove the linker sequence (CTGTAGGCACCATCAAT).
Assembly: GRCm39
Supplementary files format and content: Counts and RPKM table
Library strategy: Ribo-Seq


title: L1EEL270027_KPC1199m3_3.R1.raw.fastq.gz

description: Library name: KPC1199 ly6D overexpression-2 tissue


title: Rat_Kidney_Sham_C_DSP-1008220000001-C-F10

description:
Library name: DSP-1008220000001-C-F10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: L1EEL270025_KPC1199m3_1.R1.raw.fastq.gz

description: Library name: KPC1199 ly6D overexpression-1 tissue


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep8

description:
Library name: RNA Replicate 8 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna8


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep10

description:
Library name: RNA Replicate 10 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna10


title: L1EEL270024_KPC1199pxpr_5.R1.raw.fastq.gz

description: Library name: KPC1199 Ly6D WT-5 tissue


title: Ribo-Seq wild-type rep 1

description: Library name: RP_WT_rep1


title: Ribo-Seq mutant rep 3

description: Library name: RP_mutant_rep3


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep9

description:
Library name: RNA Replicate 9 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna9


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep7

description:
Library name: RNA Replicate 7 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna7


title: Rat_Kidney_Sham_C_DSP-1008220000001-C-C11

description:
Library name: DSP-1008220000001-C-C11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_Sham_C_DSP-1008220000001-C-C12

description:
Library name: DSP-1008220000001-C-C12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Ribo-Seq mutant rep 2

description: Library name: RP_mutant_rep2


title: Ribo-Seq wild-type rep 3

description: Library name: RP_WT_rep3


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep6

description:
Library name: RNA Replicate 6 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna6


title: Ribo-Seq mutant rep 1

description: Library name: RP_mutant_rep1


title: L1EEL270021_KPC1199pxpr_2.R1.raw.fastq.gz

description: Library name: KPC1199 Ly6D WT-2 tissue


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-C04

description:
Library name: DSP-1008220000001-C-C04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: RM-HS

value: M


title: Rat_Kidney_Sham_C_DSP-1008220000001-C-D01

description:
Library name: DSP-1008220000001-C-D01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep5

description:
Library name: RNA Replicate 5 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna5


title: L1EEL270023_KPC1199pxpr_4.R1.raw.fastq.gz

description: Library name: KPC1199 Ly6D WT-4 tissue


title: Si-B+BMN673 oligo

city: shanghai

first: yan

last: fang

address: dongchuan Street 800

institute: shanghai jiaotong university

description:
Library name: Si-B+BMN673 oligo
10× Genomics

data_processing:
In-house FASTQ files generated from 10× Genomics were aligned and quantified using Cell Ranger software (Version 6.1.2) with default settings. The output of the cell ranger and count matrix were read using the Read10× function from the Seurat package (Version 4.0.4). The merge function was used to integrate individual objects into an aggregate object, and the RenameCells function was used to ensure that all cell labels were unique.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ascites

extract_protocol:
The ascite cells were resuspended in digestion buffer (HBSS withMg2+/Ca2+ supplemented with 2 mgml collagenase type l and 40 U/ml DNase l)and incubated at 37 'C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye.ascite cells were washed in HBSS-/and resuspended in HBSS-/supplemented with 0.04% w/ BSA.
Library was performed according to the manufacter's instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix andoaded together with partitioning oil and gel beads into the chip to generate thegel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained inevery single GEM was retrotranscripted to cDNA, which contains an llumina Riprimer sequence, Unique Molecular ldentifer (UMl) and the 10x Barcode. Thepooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplifedby PCR and the apropiated sized fragments were selected with SPRlselectreagent for subsequent library construction. During the library constructionllumina R2 primer sequence, paired-end constructs with P5 and P7 sequencesand a sample index were added.

treatment_protocol: LIN28B siRNA+BMN673

value: ascites

value: tumor


title: Rat_Kidney_Sham_C_DSP-1008220000001-C-F08

description:
Library name: DSP-1008220000001-C-F08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: Sham


title: L1EEL270020_KPC1199pxpr_1.R1.raw.fastq.gz

description: Library name: KPC1199 ly6D WT-1 tissue


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep4

description:
Library name: RNA Replicate 4 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna4


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-C03

description:
Library name: DSP-1008220000001-C-C03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: R19041137-CP2-CP2-4_combined

description: Library name: Kras WT-2nd-4

data_processing:
scRNAseq reads were trimmed by fastp to remove adaptor sequences. The trimmed reads were aligned to mm10 CellRanger v3.0.0. Seraut package was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
Assembly: mm10
Supplementary files format and content: txt

source_name: pancreas

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution until processing. The tissue samples were processed as described below. Briefly, samples were first washed with PBS, minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase I  and  for 45 min at 37°C, with agitation . After digestion, samples were sieved through a 70µm 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 (Miltenyi Biotec) to lyse red blood cells.  After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA).

value: pancreas


title: Si-B+BMN673 cDNA

description:
Library name: Si-B+BMN673 cDNA
10× Genomics


title: R19041137-CP2-CP2-3_combined

description: Library name: Kras WT-2nd-3


title: R19041137-CP2-CP2-1_combined

description: Library name: Kras WT-2nd-1


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep16

description:
Library name: RNA Replicate 16 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna16

value: primary human neural progenitors

value: Vehicle (DMSO)


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep3

description:
Library name: RNA Replicate 3 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna3

value: Stimulation (CHIR)


title: Control oligo

description:
Library name: Control oligo
10× Genomics

value: PBS


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-B04

description:
Library name: DSP-1008220000001-C-B04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_Sham_C_DSP-1008220000001-C-F09

description:
Library name: DSP-1008220000001-C-F09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep15

description:
Library name: RNA Replicate 15 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna15


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-B03

description:
Library name: DSP-1008220000001-C-B03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: adipose-derived canine mesenchymal stromal cells - primary cell line 2

city: Brescia

first: Martina

last: Tambassi

state: Italy

address: Via Bianchi, 9

department: Risk Analysis and Genomic Epidemiology Unit

institute: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, VAT IT00284840170

description: Library name: Msc-C-dog2

data_processing:
The bioinformatic analysis was performed using the Galaxy platform (Galaxy Community). Specifically, reads were checked for quality by using FastQC software, version 0.12.1 and then trimmed with Trimmomatic software, version 0.39. STAR aligner version 2.7.11a was used to map the trimmed reads to the reference genome of Canis lupus familiaris CanFam3.1. Read counts per gene were then normalized with the VST method in DESeq2.
Assembly: GCA_000002285.2
Supplementary files format and content: tab-delimited text file includes VST-normalized counts for each sample

organism: Canis lupus familiaris

source_name: primary cell line

growth_protocol: Primary canine mesenchymal stromal cells were obtained form adipose tissue and maintained in an incubator at 37°C and 5% CO2 in DMEM medium supplemented with 10% fetal bovine serum, penicillin, streptomycin, and fungizone.

extract_protocol:
RNA extraction was performed using the NucleoSpin RNA II kit following manufacturer’s instructions (Macherey-Nagel, No. 740955.50). An additional DNA digestion step with rDNase in solution was performed in order to further reduce DNA contamination, followed by RNA precipitation with sodium acetate and ethanol.
The Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, San Diego, California, USA) was used to prepare transcriptomic libraries using 10 ng of RNA input. Libraries were quantified using Quantus dsDNA kit (Promega, Madison, Wisconsin) and their average fragment length was assessed using Agilent High Sensitivity D1000 kit on the Agilent TapeStation system (Agilent Technologies, Inc, Waldbronn, Germany).

treatment_protocol: Cell were seeded in 24-well plates and mantained in fisiological conditions for 48h

value: adipose tissue

value: mesenchymal stromal cells


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep2

description:
Library name: RNA Replicate 2 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna2


title: Control cDNA

description:
Library name: Control cDNA
10× Genomics


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-A03

description:
Library name: DSP-1008220000001-C-A03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-B02

description:
Library name: DSP-1008220000001-C-B02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: R19041137-CP2-CP2-2_combined

description: Library name: Kras WT-2nd-2


title: adipose-derived canine mesenchymal stromal cells - primary cell line 4

description: Library name: Msc-C-dog4


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-C02

description:
Library name: DSP-1008220000001-C-C02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-A04

description:
Library name: DSP-1008220000001-C-A04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: adipose-derived canine mesenchymal stromal cells - primary cell line 3

description: Library name: Msc-C-dog3


title: R19021447-CP-CP-3_combined

description: Library name: Kras WT-3


title: R19021447-CP-CP-4_combined

description: Library name: Kras WT-4


title: phNPC RNA ENIGMA MPRA (Stimulation) Rep1

description:
Library name: RNA Replicate 1 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : rna1


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep14

description:
Library name: RNA Replicate 14 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna14


title: adipose-derived canine mesenchymal stromal cells - primary cell line 1

description: Library name: Msc-C-dog1


title: R19021447-CP-CP-2_combined

description: Library name: Kras WT-2


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep13

description:
Library name: RNA Replicate 13 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna13


title: A53T3

city: suzhou

first: zhaotong

last: liu

address: renailu

institute: Soochow University

description: Library name: Sample 6

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). High quality reads were compared to the reference genome/transcriptome using STAR, and cirRNAs were detected and identified using DCC . CircBase database and Cire2Traits were used to annotate the identified circular RNAs. edgeR software (v3.16.5) was used to normalized the data and perform differential expressed circRNA analysis. GO and KEGG analysis were performed for the differential expressed circRNA-associated genes.
Assembly: MM39
Supplementary files format and content: EXCEL file includes CircRNA Expression Profiling

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent
CircRNA-Seq was performed by CloudSeq Inc. (Shanghai, China). Briefly, total RNAwas pretreated to enrich circRNA using CircRNA Enrichment Kit. RNA libraries were constructed by using pretreated RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs,Inc., Massachusetts, USA)according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (AgilentTechnologies,Inc., USA).Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

value: brain


title: Rat_Kidney_RM-HS_M_DSP-1008220000001-C-A02

description:
Library name: DSP-1008220000001-C-A02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

data_processing:
Raw sequencing data were processed to generate FASTQ files using GeoMx NGS Pipeline.
A gene was called detected if the signal to noise (SNR) was ≥ 4, where the limit of quantitation (LoQ) is defined as GeoMean(NegProbes)*GeoSD(NegProbes)2.
Gene counts were normalized by Q3 normalization after the removal of genes below the detection threshold.
Assembly: GRCh38 / hg38
Supplementary files format and content: target_NanoString_Q3Norm.tsv: gene expression count table with Q3 normalization in .tsv format
Library strategy: Spatial Transcriptomics


title: R19021447-CP-CP-1_combined

description: Library name: Kras WT-1


title: Rat_Kidney_RM-HS_G_DSP-1008220000001-C-E01

description:
Library name: DSP-1008220000001-C-E01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: G


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep12

description:
Library name: RNA Replicate 12 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna12


title: A53T1

description: Library name: Sample 4


title: A53T2

description: Library name: Sample 5


title: Rat_Kidney_RM-HS_G_DSP-1008220000001-C-D12

description:
Library name: DSP-1008220000001-C-D12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: R19021446-KC-KC-4_combined

description: Library name: Kras G12D mutation-4


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep11

description:
Library name: RNA Replicate 11 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna11


title: R19021446-KC-KC-3_combined

description: Library name: Kras G12D mutation-3


title: Rat_Kidney_RM-HS_G_DSP-1008220000001-C-D11

description:
Library name: DSP-1008220000001-C-D11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep10

description:
Library name: RNA Replicate 10 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna10


title: Rat_Kidney_RM-HS_G_DSP-1008220000001-C-C01

description:
Library name: DSP-1008220000001-C-C01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: R19021446-KC-KC-1_combined

description: Library name: Kras G12D mutation-1


title: Rat_Kidney_RM-HS_G_DSP-1008220000001-C-A12

description:
Library name: DSP-1008220000001-C-A12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: WT3

description: Library name: Sample 3


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep8

description:
Library name: RNA Replicate 8 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna8


title: WT1

description: Library name: Sample 1


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep7

description:
Library name: RNA Replicate 7 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna7


title: Rat_Kidney_RM-HS_G_DSP-1008220000001-C-B12

description:
Library name: DSP-1008220000001-C-B12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: R19021446-KC-KC-2_combined

description: Library name: Kras G12D mutation-2


title: Multiome, 6HPA, ATAC

city: Tübingen

first: Can

last: Aztekin

address: Max-Planck-Ring 9

department: TheFriedrich Miescher Laboratory

country: Germany

institute: The Max Planck Society for Biology

description:
Library name: 6HPA_ATAC
10X Multiomic

library_source: genomic single cell

data_processing:
Single nuclei multimodal analysis. snRNA-seq and snATAC-seq libraries were processed with CellRanger-arc software (v. 2.0.2)
Reads were aligned to the mm10 mouse genome reference dataset provided by 10x Genomics (cellranger-arc-mm10-2020-A-2.0.0).
Processed data were further analyzed using in-house R-scripts (v4.3.1) and R packages Seurat (v4.3.1) and Signac (v1.10)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5 for scRNA-seq and atac_fragments.tsv.gz,  per_barcode_metrics.csv.gz for scATAC-seq

source_name: Limb

extract_protocol:
Four to eight limbs from different time points (6, 24, 72 hpa) were pooled into an Eppendorf tube, snap-frozen on dry ice, and stored at -80°C until use. Single nuclei dissociation was conducted using a modified version of the 10x Genomics protocol (CG000365 Rev B).
Single-cell Gene Expression libraries and ATAC libraries were then prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression v1.0 (PN- 1000285) following the manufacturer's instruction (protocol CG000338 Rev F).

value: Limb

value: Epithelial cells, Schwann cells, muscle,immune cells, chondrocytes,connective tissue, etc

value: WT CD-1 mice

value: No treatment-Limb explant


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-D06

description:
Library name: DSP-1008220000001-C-D06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

source_name: Kidney

extract_protocol:
4 um Formalin-fixed paraffin-embedded rat kidney sections were used.
132 specific ROIs within 3 rats per condition (Sham, HS, RM, RM-HS) were selected for spatial transcriptomic profiling usins DSP GeoMX Nanostring technology. We manually selected regions of interest (ROIs) from four kidney areas: glomeruli (G), cortex (C), corticomedullary junction (CMJ), and medulla (M). Slides were incubated with GeoMx Mouse WTA (Nanostring) assay probe cocktail overnight. The slides were applied with morphology markers incubation before loading onto GeoMx machine.
Library preparations were carried out according to the GeoMx NGS Readout Library Prep Manual (MAN-10117; NanoString). Libraries were sequenced on an Illumina NovaSeq6000 according to the manufacturer’s instructions.

value: RM-HS

value: CMJ


title: WT2

description: Library name: Sample 2


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep9

description:
Library name: RNA Replicate 9 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna9


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep5

description:
Library name: RNA Replicate 5 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : rna5


title: Multiome, 1DPA, ATAC

description:
Library name: 1DPA_ATAC
10X Multiomic


title: Multiome, 3DPA, ATAC

description:
Library name: 3DPA_ATAC
10X Multiomic