title: C8-D1A, 42℃ incubated, 2h, 37℃ rewarmed, 6h, rep2

city: Foshan

first: Yahong

state: Guangong

address: No. 1, Jiazhi Road, Licun Village Committee, Lunjiao Subdistrict Office

department: pediatric

institute: The Eighth Affiliated Hospital of Southern MedicalUniversity(The First People's Hospital of Shunde Foshan)

description:
Library name: sample 4
The sample in fact was the exosomes extracted from the supernatant of the C8-D1A heat stress group.

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by BWA.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression were calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×10^6).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×106. Differential expression between two sets of samples was calculated byedgeR algorithm according to the criteria of |log2（Fold Change）|≥1 and P-value < 0.05.
Assembly: TargetScan, miRDB, miRTarBase and miRWalk were used to predict targets gene of selected miRNA.KOBAS was used to further Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis.
Supplementary files format and content: a separate file contains differential expression analysis results (miRNA ID, log2FC, p-value) between heat stress and control groups.

extract_protocol:
Exosomal miRNA was extracted by the MagZol (Magen) according to the manufacturer’s protocol.
The quantity and integrity of Exosomal RNA yield was assessed by using the Qubit®2.0 (Invitvogen,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, RNAs were ligated with 3’ RNA adapter, and followed by 5’ adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). The purified library products were evaluated using the Agilent 2200 TapeStation.

value: astrocytes

value: WT

value: heat stress


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-D07

status: Public on Apr 09 2026

type: SRA

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

description:
Library name: DSP-1008220000001-C-D07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

library_source: transcriptomic

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

molecule: total RNA

organism: Rattus norvegicus

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.

tag: tissue

value: Kidney

tag: group

value: RM-HS

tag: region

value: CMJ


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep6

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

country: USA

institute: UNC Chapel Hill

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

library_source: other

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)

molecule: other

organism: Homo sapiens

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).

tag: cell type

value: primary human neural progenitors

tag: treatment

value: Vehicle (DMSO)


title: C8-D1A, 37℃ incubated, 8h, rep2

last: Chen

country: China

description:
Library name: sample 2
The sample in fact was the exosomes extracted from the supernatant of the C8-D1A control group.

organism: Mus musculus

source_name: brain

value: brain

tag: cell line

tag: genotype

value: control


title: Multiome, Intact, 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: Intact_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

molecule: genomic DNA

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


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-D05

description:
Library name: DSP-1008220000001-C-D05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: C8-D1A, 37℃ incubated, 8h, rep1

description:
Library name: sample 1
The sample in fact was the exosomes extracted from the supernatant of the C8-D1A control group.


title: Multiome, 3DPA, GEX

description:
Library name: 3DPA_GEX
10X Multiomic

library_source: transcriptomic single cell

molecule: nuclear RNA

value: No treatment-Limb explant


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep4

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


title: Multiome, 6HPA, GEX

description:
Library name: 6HPA_GEX
10X Multiomic


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep1

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


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-B07

description:
Library name: DSP-1008220000001-C-B07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep2

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


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-B05

description:
Library name: DSP-1008220000001-C-B05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: primary cardiac fibroblasts, OEIRF74

city: Nanjing

first: yujia

last: xue

address: Longmian Avenue 639

institute: China Pharmaceutical University

description: Library name: sample8

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using C
Trimmed sequence reads were mapped to GrCM38/mm10using CLC genomic benchwork (parame ters-mismath cost: 2 insertion cost: 3 deletion cos st 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
RNA was harvested usina Rneasy mini plus kit(Qiagen)13 uaof total RNA was used for the construction of seauencina libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: heart

value: Fibroblast

value: TGF-b


title: primary cardiac fibroblasts, OEIRF72

description: Library name: sample6


title: primary cardiac fibroblasts, OEIRF73

description: Library name: sample7


title: Multiome, Intact, GEX

description:
Library name: Intact_GEX
10X Multiomic


title: Multiome, 1DPA, GEX

description:
Library name: 1DPA_GEX
10X Multiomic


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep16

description:
Library name: DNA Replicate 16 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna16

value: Stimulation (CHIR)


title: C8-D1A, 42℃ incubated, 2h, 37℃ rewarmed, 6h, rep1

description:
Library name: sample 3
The sample in fact was the exosomes extracted from the supernatant of the C8-D1A heat stress group.

value: astrocytes

value: WT

value: heat stress


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-A06

description:
Library name: DSP-1008220000001-C-A06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: RM-HS

value: CMJ


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-A07

description:
Library name: DSP-1008220000001-C-A07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: primary cardiac fibroblasts, OEIRF71

description: Library name: sample5


title: 1DPA, mouse limb cultured in air liquid inteface

description: Library name: Mouse_ALI

data_processing:
Mouse and Xenopus scRNA-seq samples were processed using Cell Ranger (version 8.0.1) with the GRCm39 (2024-A) mouse genome reference dataset provided by 10x Genomics Genomics (refdata-gex-GRCm39-2024-A) and the Xenopus laevis 10.1 (CRREF007_Xenopus_Laevis_v10.1_Genome), for Xenopus samples.
Assembly: GRCm39
Assembly: CRREF007_Xenopus_Laevis_v10.1_Genome
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: barcodes, genes, and matrix files.  barcodes_AERfactors.tsv (-1_1 = VehCtrl_96w, -1_2 = AER_96w, -1_3 = AER_ALI), barcodes_Mouse_ALI_vs_96w.tsv (-1_1 = ALI, -1_2 = 96w), barcodes_Xen_ALI_vs_96w.tsv (-1_1 = ALI, -1_2 = 96w).

source_name: limb explants

extract_protocol:
5 to 6 limb explants for 1 dpa were pooled in an Eppendorf tube and immediately processed for dissociation.
Single-cell Gene Expression libraries were then prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000268) following the manufacturer's instruction (protocol CG000315 Rev C).

treatment_protocol: 100 ng/mL BMP4 (PeproTech, 120-05ET), 100 ng/mL FGF10 (PeproTech, 100-26), 3 µM CHIR99021 (Calbiochem, 361559), and 100 ng/mL EGF (Thermo Scientific, AF-100-15). CHIR99021 was prepared in DMSO (Thermo Scientific, BP231-100) and recombinant proteins were prepared according to manufacturer’s recommendations. The vehicle control had the volume matched DMSO and according to the vehicle of the recombinant protein batches. All molecules were diluted in media and maintained throughout the duration of the experiment, with fresh cocktail added during media changes once every 2 days.

value: limb explants


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep15

description:
Library name: DNA Replicate 15 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna15

value: primary human neural progenitors


title: phNPC RNA ENIGMA MPRA (Vehicle) Rep3

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

value: Vehicle (DMSO)


title: Rat_Kidney_RM-HS_CMJ_DSP-1008220000001-C-A05

description:
Library name: DSP-1008220000001-C-A05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-D10

description:
Library name: DSP-1008220000001-C-D10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: C


title: primary cardiac fibroblasts, GFP4

description: Library name: sample4


title: 1DPA, mouse limb cultured in 96 well plate

description: Library name: Mouse_96w

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

value: WT CD-1 mice


title: primary cardiac fibroblasts, GFP3

description: Library name: sample3


title: 3DPA AER Inducing cocktail, mouse limb cultured in air liquid interface

description: Library name: Mouse_AER_ALI

value: AER induction (BMP4 , FGF10, CHIR99021, and EGF)


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-D09

description:
Library name: DSP-1008220000001-C-D09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-D08

description:
Library name: DSP-1008220000001-C-D08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep12

description:
Library name: DNA Replicate 12 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna12


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep13

description:
Library name: DNA Replicate 13 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna13


title: 3DPA AER Inducing cocktail, mouse limb cultured in 96 well plate

description: Library name: Mouse_AER_96w


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-B10

description:
Library name: DSP-1008220000001-C-B10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 3DPA Vehicle control mouse limb

description: Library name: Mouse_VehCtrl_96w


title: primary cardiac fibroblasts, GFP1

description: Library name: sample1

value: heart


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-B09

description:
Library name: DSP-1008220000001-C-B09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: primary cardiac fibroblasts, GFP2

description: Library name: sample2

value: Fibroblast


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep14

description:
Library name: DNA Replicate 14 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna14


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-B08

description:
Library name: DSP-1008220000001-C-B08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Intrathoracic adhesion tissues, 9 days after talc administration, Day9_4

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

country: Japan

institute: Ehime University

description: Library name: D9_4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality: 0.05)
Trimmed Sequence reads were mapped to GRCm38 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: Adhesion tissue between the chest wall and lungs

growth_protocol: After the mice were sedated, 200 μL of a saline-based talc solution (2.0 g/kg) was administered into the left thoracic cavity through the diaphragm with a 24-gauge needle.

extract_protocol:
Total RNA was harvested using QIAGEN miRNeasy Micro Kit (QIAGEN).
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magenetic Isolation Module (NEB E7490) and NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols. (https://www.neb.com/ja-jp/protocols/2014/12/01/protocol-for-use-with-nebnext-poly-a-mrna-magnetic-isolation-module-neb-e7490)

treatment_protocol: At 30 minutes, 3 days, and 9 days post-injection, the mice were sacrificed. Immediately after euthanasia, RNA was extracted from the left lung parenchyma, which is connected to the chest.

value: Administration of talc solution into the left thoracic cavity


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep9

description:
Library name: DNA Replicate 9 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna9

value: Stimulation (CHIR)


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep10

description:
Library name: DNA Replicate 10 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna10


title: SIHK1-SMAD3

description:
Library name: sample8
TGF-vs-siHK1_SMAD3_final_anno.txt

data_processing:
Removing reads containing adapters;
Removing reads containing more than 10% of unknown nucleotides (N); Removing reads containing adapters;Removing reads containing more than 10% of unknown nucleotides (N); Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
BWA (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak B WA[1] (version 0.7.12) using default parameters was used to align the clean reads from each sample against the reference genome, and only the alignments within 2 mismatches were considered in peak  scanning.
Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics. It is based on the fact that a high quality IP-seq experiment produces significant clustering of enriched DNA sequence tags at locations bound by the protein of interest, and that the sequence tag density accumulates on forward and reverse strands centered around the binding site. SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
MACS (version: macs14)( -p 1e-3 -m 10,30) is a computational method that was designed to identify read-enriched regions from ChIP-seq data. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value<1e-5. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number were displayed.
Assembly: mm10
Supplementary files format and content: final_anno.txt
Library strategy: CUT&Tag

extract_protocol:
ConA Beads Pro intended for nucleus binding and DNA Extract Beads Pro intended for DNA extraction by using Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro TD904ConA Beads Pro intended for nucleus binding and DNA Extract Beads Pro intended for DNA extraction by using Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro TD904
VAHTS DNA Clean Beads (Vazyme #N411) is used for library purification.10 ng of DNA was used as startnig material for input amout. Libraries were amplified using 10 cycles on thr thermocycle.

value: TGF-b


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-A10

description:
Library name: DSP-1008220000001-C-A10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: SIHK1-JUN

description:
Library name: sample10
TGF-vs-siHK1_JUN_final_anno.txt


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep8

description:
Library name: DNA Replicate 8 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna8


title: Intrathoracic adhesion tissues, 9 days after talc administration, Day9_1

description: Library name: D9_1

value: Adhesion tissue between the chest wall and lungs

value: WT


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep11

description:
Library name: DNA Replicate 11 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna11


title: Intrathoracic adhesion tissues, 3 days after talc administration, Day3_4

description: Library name: D3_4


title: Intrathoracic adhesion tissues, 9 days after talc administration, Day9_3

description: Library name: D9_3


title: TGF-SMAD3

description:
Library name: sample7
TGF-vs-siHK1_SMAD3_final_anno.txt


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep7

description:
Library name: DNA Replicate 7 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna7


title: TGF-JUN

description:
Library name: sample9
TGF-vs-siHK1_JUN_final_anno.txt


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep6

description:
Library name: DNA Replicate 6 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna6


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-A09

description:
Library name: DSP-1008220000001-C-A09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney


title: Intrathoracic adhesion tissues, 3 days after talc administration, Day3_1

description: Library name: D3_1


title: SIHK1-NFATC2

description:
Library name: sample6
TGF-vs-siHK1_NFATC2_final_anno.txt


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep5

description:
Library name: DNA Replicate 5 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna5


title: Intrathoracic adhesion tissues, 30minutes after talc administration, Day0_3

description: Library name: D0_3


title: Rat_Kidney_RM_M_DSP-1008220000001-C-H07

description:
Library name: DSP-1008220000001-C-H07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: RM

value: M


title: Rat_Kidney_RM-HS_C_DSP-1008220000001-C-A08

description:
Library name: DSP-1008220000001-C-A08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: RM-HS


title: SI H3K9LC

description:
Library name: sample4
TGF-vs-siHK1_H3K9lc_final_anno.txt


title: Intrathoracic adhesion tissues, 3 days after talc administration, Day3_3

description: Library name: D3_3


title: TGF-NFATC2

description:
Library name: sample5
TGF-vs-siHK1_NFATC2_final_anno.txt


title: Rat_Kidney_RM_M_DSP-1008220000001-C-H06

description:
Library name: DSP-1008220000001-C-H06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep4

description:
Library name: DNA Replicate 4 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna4

value: primary human neural progenitors


title: Rat_Kidney_RM_M_DSP-1008220000001-C-H05

description:
Library name: DSP-1008220000001-C-H05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Intrathoracic adhesion tissues, 30minutes after talc administration, Day0_2

description: Library name: D0_2


title: TGF H3K9LC

description:
Library name: sample3
TGF-vs-siHK1_H3K9lc_final_anno.txt


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep3

description:
Library name: DNA Replicate 3 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna3


title: NC (control)

description:
Library name: sample2
NC-vs-TGF_H3K9lc_final_anno.txt


title: Rat_Kidney_RM_M_DSP-1008220000001-C-G04

description:
Library name: DSP-1008220000001-C-G04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep2

description:
Library name: DNA Replicate 2 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna2


title: TGF

description:
Library name: sample1
TGF_final_anno.txt


title: Rat_Kidney_RM_M_DSP-1008220000001-C-G03

description:
Library name: DSP-1008220000001-C-G03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: ABA29934

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: 3T3-L1 cells differentiated into adipocytes

data_processing:
Image analysis, base calling, and quality scoring of the run were processed using the manufacturer’s Real Time Analysis (RTA 3.4.4) software, followed by the generation of FASTQ sequence files. RNA-seq reads were mapped against the Homo sapiens (GRCh38) and Mus musculus (GRCm39) reference genomes with STAR/2.7.8a using ENCODE parameters. Gene quantification was performed with RSEM/1.3.0 using gencode.v42 and gencode.vM31 annotations. Differential expression analysis was performed with limma using the voom transformation of the counts. Functional enrichment of the differentially expressed genes was performed using g:Profiler.
Assembly: hg38
Supplementary files format and content: Processed data diles include the log of counts (logcpm)

extract_protocol:
Cells were washed twice with ice-cold PBS and lysed using TRIzol reagent (15596018, Invitrogen). Lysates were then mixed with 200 μl of chloroform, vortexed, and incubated for 2 min at RT. Samples were then centrifuged at 12,000 x g for 20 min at 4°C. The aqueous phase was transferred into a new Eppendorf tube and mixed with 500 μl of RNase-free isopropanol. Eppendorfs were incubated for 15 min at RT and centrifuged at 12,000 x g for 20 min at 4° to precipitate RNA. Supernatant was discarded, and the pellet was washed with 1 ml ethanol 75% and centrifuged at 12,000 x g for 20 min at 4°C. Ethanol was completely removed, and the RNA pellet was resuspended in 20-60 μl RNase-free water. Samples were then quantified using a NanoDrop. Total RNA was quantified using the Qubit® RNA BR Assay Kit (Thermo Fisher Scientific) and RNA integrity was assessed using the RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The RNA-Seq libraries were prepared with the KAPA Stranded mRNA-Seq Kit for Illumina Platforms (Roche) according to the manufacturer’s recommendations. Briefly, 500 ng of total RNA was used for poly-A fraction enrichment. The blunt-ended double-stranded cDNA was 3’-adenylated, and Illumina platform-compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was then enriched through 15 cycles of PCR, and the final library was validated using an Agilent 2100 Bioanalyzer with the DNA 7500 Assay. The libraries were sequenced on a NovaSeq 6000 (Illumina) in paired-end mode with a read length of 2x51 bp, following the manufacturer’s protocol for dual indexing.

value: 3T3-L1 cocultured with MCF7


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep16

description:
Library name: DNA Replicate 16 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna16

value: Vehicle (DMSO)


title: phNPC DNA ENIGMA MPRA (Stimulation) Rep1

description:
Library name: DNA Replicate 1 (Stimulation)
Column name in bc_raw.counts.Stim.csv.gz : dna1


title: ABA29932


title: C57BL/6, E10_775

city: Jerusalem

first: Batia

last: Azria

state: Israel

address: Jerusalem

country: Israel

institute: Hebrew university of Jerusalem

description: Library name: E10_775

library_source: genomic

data_processing:
RRBS data were trimmed and quality filtered by trim galore software using default parameters for RRBS. Reads were mapped against mm10 reference genome with Bismark and analyzed using wgbstools (Loyfer and Kaplan). The ENCODE mm10 blacklist was used to filter problematic genomic regions in the RRBS data.
To accurately identify sequence-dependent allele-specific methylation (SD-ASM) loci and prevent misidentification due to CpG-to-non-CpG variants between strains, we implemented stringent filtering criteria. For a CpG site to be considered methylated, a minimum of five DNA fragments were required on both the forward and reverse strands. Furthermore, differential methylation between the two compared strains was required on both the forward and reverse strand fragments.
Assembly: mm10
Supplementary files format and content: Beta

extract_protocol:
DNA was isolated from fresh mouse tissues (Liver and cerebellum) or from isolated cells (wight fat cells and colon epithelium cells). All tissues or cells incubated in lysis buffer (25 mM Tris-HCl (pH 8), 2 mM ethylenediaminetetraacetic acid, 0.2% sodium dodecyl sulfate, 200 mM NaCl) supplemented with 300 μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation
Bisulfite-seq reduced representation

tag: strain


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep15

description:
Library name: DNA Replicate 15 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna15


title: Rat_Kidney_RM_M_DSP-1008220000001-C-G02

description:
Library name: DSP-1008220000001-C-G02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: ABA29933


title: Rat_Kidney_RM_M_DSP-1008220000001-C-E04

description:
Library name: DSP-1008220000001-C-E04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: ABA29931

value: untreated


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep14

description:
Library name: DNA Replicate 14 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna14


title: Intrathoracic adhesion tissues, 30minutes after talc administration, Day0_1

description: Library name: D0_1


title: C57BL/6, E10_772

description: Library name: E10_772


title: ABA29930


title: C57BL/6, E10_774

description: Library name: E10_774


title: Rat_Kidney_RM_M_DSP-1008220000001-C-E02

description:
Library name: DSP-1008220000001-C-E02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep13

description:
Library name: DNA Replicate 13 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna13


title: Rat_Kidney_RM_M_DSP-1008220000001-C-E03

description:
Library name: DSP-1008220000001-C-E03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: C57BL/6, E10_771

description: Library name: E10_771


title: ABA29929


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep12

description:
Library name: DNA Replicate 12 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna12


title: Rat_Kidney_RM_G_DSP-1008220000002-A-A02

description:
Library name: DSP-1008220000002-A-A02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: G


title: C57BL/6, Liver_826

description: Library name: Liver_826

source_name: Liver

value: Liver


title: Rat_Kidney_RM_G_DSP-1008220000001-C-H12

description:
Library name: DSP-1008220000001-C-H12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: PBS_PBS3

city: Freiburg

first: Philipp

last: Henneke

state: Baden-Württemberg

address: Breisacher Straße 115 B

department: Institute for Infection Prevention and Control (IIK)

institute: University Hospital Freiburg

data_processing:
Illumina bcl2fastq (2.20) was used for demultiplexing of the reads. Adaptor trimming was performed with Skewer (0.2.2) and alignment was done with STAR (2.7.3) against mm10
Data was analysed in R (4.3.2) with DESeq2. Genes with row sums below 2 were excluded.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes normalized counts after DESeq2 analysis

source_name: liver

growth_protocol: SPF animal facility

extract_protocol:
Livers were isolated and digested 4 weeks after injection of PBS or BCG-BFP. Kupffer cells were sorted by flow cytometry and RNA was extracted with the ExtractMe Total RNA Micro Spin Kit (Blirt)
Libraries were prepared using 1ng RNA with the Library Preparation Kit SMART-Seq Stranded (Takara Bio)

treatment_protocol: Mice received either i.v. injection of BCG-BFP (107 cfu) or PBS in 100µl

value: liver

value: Kupffer cell

tag: time

value: 4 weeks post injection

tag: mouse

tag: antibody

value: tdTom+ Tim4+

value: PBS i.v. injection


title: C57BL/6, Liver_821

description: Library name: Liver_821


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep11

description:
Library name: DNA Replicate 11 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna11


title: C57BL/6, Liver_822

description: Library name: Liver_822


title: PBS_PBS1


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep9

description:
Library name: DNA Replicate 9 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna9


title: Rat_Kidney_RM_G_DSP-1008220000001-C-G11

description:
Library name: DSP-1008220000001-C-G11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: C57BL/6, Fat_822

description: Library name: Fat_822

source_name: Fat

value: Fat


title: Rat_Kidney_RM_G_DSP-1008220000001-C-H11

description:
Library name: DSP-1008220000001-C-H11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep10

description:
Library name: DNA Replicate 10 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna10


title: Rat_Kidney_RM_G_DSP-1008220000001-C-G12

description:
Library name: DSP-1008220000001-C-G12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM_G_DSP-1008220000001-C-H01

description:
Library name: DSP-1008220000001-C-H01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Tim4-_BCG3

value: tdTom+ Tim4-

value: BCG i.v. infection


title: C57BL/6, Fat_821

description: Library name: Fat_821


title: TIm4-_BCG2


title: PBS_PBS2


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep8

description:
Library name: DNA Replicate 8 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna8


title: C57BL/6, Liver_820

description: Library name: Liver_820


title: Tim4-_BCG1


title: C57BL/6, Fat_826

description: Library name: Fat_826


title: Rat_Kidney_RM_G_DSP-1008220000001-C-F01

description:
Library name: DSP-1008220000001-C-F01
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: RM


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep7

description:
Library name: DNA Replicate 7 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna7


title: C57BL/6, Fat_820

description: Library name: Fat_820


title: low_BCG3

value: tdTom- Tim4+


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep6

description:
Library name: DNA Replicate 6 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna6

value: primary human neural progenitors


title: high_BCG2


title: low_BCG1


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep4

description:
Library name: DNA Replicate 4 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna4


title: low_BCG2


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep2

description:
Library name: DNA Replicate 2 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna2


title: high_BCG3


title: Rat_Kidney_RM_G_DSP-1008220000001-C-E12

description:
Library name: DSP-1008220000001-C-E12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: C57BL/6, Colon_826

description: Library name: Colon_826

source_name: Colon

value: Colon


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-G07

description:
Library name: DSP-1008220000001-C-G07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: CMJ


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-G06

description:
Library name: DSP-1008220000001-C-G06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: C57BL/6, Colon_821

description: Library name: Colon_821


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep5

description:
Library name: DNA Replicate 5 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna5

value: Vehicle (DMSO)


title: C57BL/6, Cerebellum_822

description: Library name: Cerebellum_822

source_name: Cerebellum

value: Cerebellum


title: C57BL/6, Cerebellum_826

description: Library name: Cerebellum_826


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-H04

description:
Library name: DSP-1008220000001-C-H04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep1

description:
Library name: DNA Replicate 1 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna1


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-H03

description:
Library name: DSP-1008220000001-C-H03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: C57BL/6, Colon_822

description: Library name: Colon_822


title: phNPC DNA ENIGMA MPRA (Vehicle) Rep3

description:
Library name: DNA Replicate 3 (Vehicle)
Column name in bc_raw.counts.Veh.csv.gz : dna3


title: high_BCG1


title: H9 DIV100 SpOrg - Sample C

city: cambridge

first: Andras

last: Lakatos

state: cambridgeshire

address: Cambridge Centre For Brain Repair, Ed Adrian Building

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample C
10X Genomics

data_processing:
Samples were pooled and sequenced on 1 lane of a NovaSeq 6000. Output files were converted to fastq using bcl2fastq. CellRanger's (3.0.0) 'count' function was used to align reads to the GRCh38 human genome.
Assembly: GRCh38
Supplementary files format and content: Tab-value separates data files and matrix files.

source_name: organoid

growth_protocol: Spinal Organoids were grown as described in the manuscript. In brief hESC aggregates were treated with CHIR99021, FGF-2, SAG, and retinoic acid to direct aggregates to a spinal fate. These organoids were then sliced at DIV25 and further cultured in slice media (Neurobasal Media + B27 + GDNF + BDNF + IGF-1) till DIV100 when they were prepared for sequencing.

extract_protocol:
Organoids were dissociated using papain (Worthington) on the gentleMACs octodissociator (Miltenyi; ABDK settings)
Single cell libraries were prepared in accordance with the manufacturer using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics, 1000269) with a 10X Chromium Controller (10X Genomics, 1000204). In brief, the previously dissociated cell mixture and kit Mastermix was loaded onto a Chromium Single cell 3′ chip (estimated capture of 10,000 cells) to generate a gel beads in emulsion (GEM) mixture. A reverse transcriptase reaction was then carried out to generate a barcoded cDNA library using C1000 Touch Thermal Cycler (Biorad, 12 cycles of amplification). Quality control of samples was performed using a 2100 Bioanalyzer Instrument (Agilent) before further processing. For sequencing, samples were pooled and ran on an Illumina NovaSeq 6000.

value: organoid

value: H9 hESC

value: control

tag: batch


title: C57BL/6, Colon_820

description: Library name: Colon_820


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-G05

description:
Library name: DSP-1008220000001-C-G05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM_G_DSP-1008220000001-C-E11

description:
Library name: DSP-1008220000001-C-E11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: G


title: H9 DIV100 SpOrg - Sample B

description:
Library name: Sample B
10X Genomics


title: C57BL/6, Cerebellum_821

description: Library name: Cerebellum_821


title: 53BP1_KO_3

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description: 53BP1 knockout, Emu-Bcl2\, RAG1 deficient

data_processing:
Reads were aligned using bowtie 2.2.8 with --local flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Assembly: mm9
Supplementary files format and content: wig files contain peak information for samples
Library strategy: PRO-Seq

source_name: v-Abl transformed pro-B cell line

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with permeabilization buffer. The permeabilized cells were resuspended in 100 ml of storage buffer for nuclear run-on with 2X run-on mix at 37℃ for 5 min. RNA was extracted by Trizol and followed by hybrolyzation. The RNA was incubated with streptavidin C1 beads (Thermo Fisher Scientific, #65001) and the enriched run-on samples were incubated with hydroxyl repair with T4 PNK (NEB, M0201S) and RppH (NEB, M0356S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA.
The cDNA was subjected to making PRO-seq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318). PRO-seq libraries were sequenced via single end 50bp or paired end 150bp sequencing on a Nova-seq 6000 (Illumina) sequencer and normalized to a coverage of 10 million 100nt reads for display.

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.

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: C57BL/6, Cerebellum_820

description: Library name: Cerebellum_820


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-E06

description:
Library name: DSP-1008220000001-C-E06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: ABA29943

value: MCF7 cocultured with 3T3-L1


title: 53BP1_KO_2

value: 53BP1 knockout, Emu-Bcl2\, RAG1 deficient


title: H9 DIV100 SpOrg - Sample A

description:
Library name: Sample A
10X Genomics


title: 129X1/Sv, Liver_819

description: Library name: Liver_819

value: Liver


title: 53BP1_KO_1


title: WT_3

description: Emu-Bcl2\, RAG1 deficient

value: Emu-Bcl2\, RAG1 deficient


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-E07

description:
Library name: DSP-1008220000001-C-E07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: RM


title: 129X1/Sv, Liver_818

description: Library name: Liver_818


title: ABA29942


title: Rat_Kidney_RM_CMJ_DSP-1008220000001-C-E05

description:
Library name: DSP-1008220000001-C-E05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM_C_DSP-1008220000001-C-H10

description:
Library name: DSP-1008220000001-C-H10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: C


title: WT_2

description: Emu-Bcl2\, RAG1 deficient


title: Rat_Kidney_RM_C_DSP-1008220000001-C-H09

description:
Library name: DSP-1008220000001-C-H09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: ABA29940

value: untreated


title: WT_1

description: Emu-Bcl2\, RAG1 deficient


title: ABA29939


title: Rat_Kidney_RM_C_DSP-1008220000001-C-H08

description:
Library name: DSP-1008220000001-C-H08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 129X1/Sv, Liver_816

description: Library name: Liver_816


title: 129X1/Sv, Liver_817

description: Library name: Liver_817


title: 129X1/Sv, Fat_818

description: Library name: Fat_818

value: Fat


title: 53BP1_KO_Rad21_2

data_processing:
Reads were aligned using bowtie 2.4.4 with --very-sensitive flag
reads were quantified for specific loci using samtools 1.15.1
wig files were produced using bamCoverage 3.5.1 and normalized using RPKM
peak files were produced using MACS2 2.2.7.1
Assembly: mm9
Supplementary files format and content: wig files contain peak information for samples
Supplementary files format and content: peak files contain enriched peak information for samples using MACS2

extract_protocol:
20 million RAG-deficient v-Abl cells treated with STI-571 for 4 days were collected, fixed with 1% formaldehyde for 10 min at room temperature, and quenched with glycine at a final concentration of 125 mM. The pellet was sonicated with a Covaris M220 sonicator for 5-8 min in sonication buffer until the size of most fragments was in the range of 200–700 bp. 25ug sonicated chromatin was then brought to RIPA-LS buffer conditions. The antibody was added by rotating overnight at 4 °C. For each immunoprecipitation, 25 μl magnetic Protein A (Invitrogen, 10002D) were washed twice and resuspended in 500ul PBS supplemented with 5mg/ml BSA and incubate 4°C overnight to block beads. The blocked beads were added and bound to antibody by rotating 2 h at 4 °C. Used antibodies were Rad21 (0.2 μg per immunoprecipitation, abcam, ab992). Beads were washed subsequently with RIPA-LS (twice), RIPA-HS (twice) , RIPA-LiCl (twice) and 10 mM Tris pH 8.0 (once) to remove detergent, salts and EDTA. Beads were resuspended in 25 μl of the tagmentation reaction mix containing 1 μl Tagment DNA Enzyme and incubated at 37 °C for 5-10 min in a thermocycler. The beads were washed with RIPA-LS (twice) and once with TE. And then de-crosslinked with Proteinase K (Roche, #03115852001).
ChIP DNA was purified with SPRI AMPure XP beads. 20ul Purified DNA (from above), 25μl High-Fidelity 2X PCR Master Mix (NEB, M0541), 2.5 μl N5xx (Vazyme, TD202), 2.5 μl N7xx (Vazyme, TD202). PCR was set up as follows: 98 °C, 30 s; [98 °C, 10 s, 60 °C, 20 s, 72 °C, 20 s] × 10-14 cycles; 4 °C hold. The amplified libraries were purified by AmpureXP beads and were sequenced via paired end 150bp sequencing on a NovaSeq 6000 (Illumina) sequencer.

value: 53BP1 antibody(NB100-304), 3 uM STI-571 treated for 4 days


title: ABA29938


title: Rat_Kidney_RM_C_DSP-1008220000001-C-G09

description:
Library name: DSP-1008220000001-C-G09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: ABA29941


title: WT_Rad21_2

description: Emu-Bcl2\, RAG1 deficient


title: WT_Rad21_1

description: Emu-Bcl2\, RAG1 deficient


title: 53BP1_KO_Rad21_1


title: AML#65 cells from patient

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

data_processing:
RNA-seq reads were trimmed with AdapterRemoval (v 2.1.7), aligned to hg38 genome by STAR (v 2.6.1). For PDX samples, murine reads were removed by disambiguate tool, adopting mm39 as reference. Samtools (v 1.9) was run to remove duplicates and indexing. Raw counts were obtained using htseq-count and Ensembl95 genes
Assembly: hg38
Supplementary files format and content: Files in tab-delimited format containing raw counts

source_name: BM

extract_protocol:
RNA was harvested using Trizol reagent and following  manufacturer's protocol
RNA libraries for RNA-seq were prepared by using NEB Next Ultra II, with RiboZero Plus kit, following the manufacturer's protocol.

value: BM

tag: tumor stage

value: Patient

value: Primary AML blasts


title: 129X1/Sv, Fat_819

description: Library name: Fat_819


title: Rat_Kidney_RM_C_DSP-1008220000001-C-G10

description:
Library name: DSP-1008220000001-C-G10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#62 cells from patient


title: 129X1/Sv, Fat_817

description: Library name: Fat_817


title: Rat_Kidney_RM_C_DSP-1008220000001-C-G08

description:
Library name: DSP-1008220000001-C-G08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 129X1/Sv, Colon_819

description: Library name: Colon_819

value: Colon


title: ATAC_53BP1_KO_3

extract_protocol:
Sample were extracted according to Illumina's instructions accompanying Hyperactive ATAC-Seq Library Prep Kit for Illumin (Vazyme, TD711)
Libraries were prepared according to Illumina's instructions accompanying Hyperactive ATAC-Seq Library Prep Kit for Illumin (Vazyme, TD711)


title: Rat_Kidney_RM_C_DSP-1008220000001-C-E10

description:
Library name: DSP-1008220000001-C-E10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 129X1/Sv, Fat_816

description: Library name: Fat_816


title: AML#46 cells from P3-PDX

source_name: SPLEEN

value: SPLEEN

value: PDX


title: AML#46 cells from P1-PDX


title: ATAC_53BP1_KO_2

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: ATAC_53BP1_KO_1

value: 53BP1 knockout, Emu-Bcl2\, RAG1 deficient


title: Rat_Kidney_RM_C_DSP-1008220000001-C-E08

description:
Library name: DSP-1008220000001-C-E08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 129X1/Sv, Colon_818

description: Library name: Colon_818


title: 129X1/Sv, Cerebellum_819

description: Library name: Cerebellum_819

value: Cerebellum


title: AML#46 cells from P2-PDX


title: ATAC_WT_3

description: Emu-Bcl2\, RAG1 deficient

value: Emu-Bcl2\, RAG1 deficient


title: Rat_Kidney_HS_M_DSP-1010707202201-E-D07

description:
Library name: DSP-1010707202201-E-D07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

value: HS

value: M


title: Rat_Kidney_HS_M_DSP-1010707202201-E-D06

description:
Library name: DSP-1010707202201-E-D06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_RM_C_DSP-1008220000001-C-E09

description:
Library name: DSP-1008220000001-C-E09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: RM

value: C


title: AML#46 cells from P0-PDX


title: 129X1/Sv, Colon_817

description: Library name: Colon_817


title: ATAC_WT_2

description: Emu-Bcl2\, RAG1 deficient


title: 129X1/Sv, Cerebellum_818

description: Library name: Cerebellum_818


title: Rat_Kidney_HS_M_DSP-1010707202201-E-D05

description:
Library name: DSP-1010707202201-E-D05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#43 cells from P2-PDX


title: 53BP1_KO_iEμ_3

description: iEu bait, 53BP1 knockout, Emu-Bcl2\, RAG1 deficient

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.
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: bedgraph files were generated for displaying (Jane et al., 2018)
Library strategy: 3C-HTGTS

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with DpnⅡ enzyme (NEB, R0543) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018).

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


title: ATAC_WT_1

description: Emu-Bcl2\, RAG1 deficient


title: Rat_Kidney_HS_M_DSP-1010707202201-E-B07

description:
Library name: DSP-1010707202201-E-B07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#46 cells from patient

value: BM


title: AML#43 cells from patient

value: Patient


title: 129X1/Sv, Cerebellum_817

description: Library name: Cerebellum_817


title: 129X1/Sv, Cerebellum_816

description: Library name: Cerebellum_816


title: AML#42 cells from P3-PDX

value: Primary AML blasts


title: Rat_Kidney_HS_M_DSP-1010707202201-E-B06

description:
Library name: DSP-1010707202201-E-B06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_HS_M_DSP-1010707202201-E-B05

description:
Library name: DSP-1010707202201-E-B05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: 53BP1_KO_iEμ_2


title: SC481

city: Pittsburgh

first: Kathryn

last: Torok

email: TRH107@pitt.edu, kst7@pitt.edu

state: PA

address: 4401  Penn Ave

institute: University of Pittsburgh

description:
Library name: Sample 10
processed data file: filtered_feature_bc_matrix.h5

data_processing:
CellRanger
Seurat
Assembly: GRCh38
Supplementary files format and content: combined matrix of all SC (sans FLEX) samples in this study

source_name: Skin

extract_protocol:
Miltenyi Biotec Whole Skin Dissociation Kit Human
10X Genomics Single Cell RNA Seq 3 Prime V2 Libraries

value: Skin

tag: disease state

value: Healthy

tag: onset

value: Pediatric


title: 53BP1_KO_iEμ_1

value: v-Abl transformed pro-B cell line


title: WT_iEμ_3

description: iEubait, Emu-Bcl2\, RAG1 deficient


title: SC524

description:
Library name: Sample 9
processed data file: filtered_feature_bc_matrix.h5

value: SSc


title: Rat_Kidney_HS_G_DSP-1010707202201-E-E08

description:
Library name: DSP-1010707202201-E-E08
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: G


title: SC522

description:
Library name: Sample 8
processed data file: filtered_feature_bc_matrix.h5


title: Rat_Kidney_HS_G_DSP-1010707202201-E-D12

description:
Library name: DSP-1010707202201-E-D12
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: SC507

description:
Library name: Sample 11
processed data file: filtered_feature_bc_matrix.h5


title: WT_iEμ_1

description: iEu bait, Emu-Bcl2\, RAG1 deficient


title: Rat_Kidney_HS_G_DSP-1010707202201-E-E10

description:
Library name: DSP-1010707202201-E-E10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#42 cells from P1-PDX

value: SPLEEN

value: PDX


title: Rat_Kidney_HS_G_DSP-1010707202201-E-D11

description:
Library name: DSP-1010707202201-E-D11
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney


title: LM2

city: Wenzhou

first: Hui

state: Zhejiang

address: Xueyuan west road number 109

institute: The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps. Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed. Software CutAdapter, parameters -o 5 -p 100
Read alignment software, software HISAT, version 2.0, parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts. Software StringTie, version 1.3.0, parameters -b dta -q phred33-quals.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts and FPKM values for each Sample.

source_name: lung

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: lung

value: WT


title: AML#35 cells from P2-PDX


title: AML#33 cells from P2-PDX


title: WT_iEμ_2

description: iEu bait, Emu-Bcl2\, RAG1 deficient

value: Emu-Bcl2\, RAG1 deficient


title: AML#33 cells from patient


title: AML#42 cells from patient

source_name: PB

value: PB


title: SC360

description:
Library name: Sample 4
processed data file: filtered_feature_bc_matrix.h5


title: LM1


title: AML#42 cells from P2-PDX


title: AML#42 cells from P0-PDX


title: SC419

description:
Library name: Sample 7
processed data file: filtered_feature_bc_matrix.h5


title: LM3


title: SC416

description:
Library name: Sample 6
processed data file: filtered_feature_bc_matrix.h5


title: M3


title: Rat_Kidney_HS_G_DSP-1010707202201-E-B12

description:
Library name: DSP-1010707202201-E-B12
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

value: HS


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-E03

description:
Library name: DSP-1010707202201-E-E03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: CMJ


title: SC367

description:
Library name: Sample 5
processed data file: filtered_feature_bc_matrix.h5


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-E04

description:
Library name: DSP-1010707202201-E-E04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-E02

description:
Library name: DSP-1010707202201-E-E02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#31 cells from P2-PDX


title: AML#31 cells from P3-PDX


title: FMRP-cTag CLIP, CA1, Control, 5 minutes, replicate 4

city: New York

first: Ruth

middle: A

last: Singer

state: NY

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

description: Library name: FMRP_CLIP_Control_5min_rep4

data_processing:
Filter for quality of reads using fastq_filter.pl (CTK, fastq_filter.pl -f min:0-15:20,mean:16-39:20)
Trim 3' linker sequence (Cutadapt, -m 20 -a GTGTCAGTCACTTCCAGCGG)
Collapse exact duplicates using fastq2collapse.pl (CTK). Trim 5' barcode and linker (CTK, stripBarcode.pl -len 9)
Remove reads less than 17 nt prior to mapping (cutadapt -m 17)
Mapped reads with STAR to UCSC mm10 transcriptome
Assembly: Collapse PCR duplicates (CTK, tag2collapse.pl -EM 30 -random-barcode --seq-error-model em-local --weight-in-name --keep-max-score --keep-tag-name)
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files contain quantification of the numer of FMRP tags mapped per transcript

source_name: CA1 hippocampus

extract_protocol:
After optogenetic activation and UV-crosslinking, tissue was dissected from acute hippocampal slices in HBSS with 0.1 mg/mL cycloheximide. Tissue was homogenized in lysis buffer (1x PBS, 0.1% SDS, 0.5% NP-40, 0.5% Sodium deoxycholate supplemented, 1X cOmplete Mini EDTA-free Protease Inhibitor (Roche) and 0.1 mg/mL cycloheximide) by mechanical homogenization. FMRP-cTag-CLIP was performed as described previously (see associated paper for details).
RNA tags were isolated and cloned using the BrdU-CLIP method as described in associated paper.

value: CA1 hippocampus

value: Camk2a-Cre x Fmr1 cTag

value: AAV-Control

tag: time post_activation

tag: previous file_name

value: N/A- new files


title: SC288

description:
Library name: Sample 3
processed data file: filtered_feature_bc_matrix.h5

tag: tissue

value: Skin

value: Pediatric


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-D03

description:
Library name: DSP-1010707202201-E-D03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

tag: group


title: C3

value: PBS


title: M2


title: AML#31 cells from patient

value: BM

value: Patient

value: Primary AML blasts


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-D04

description:
Library name: DSP-1010707202201-E-D04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney

tag: region


title: AML#31 cells from P0-PDX

value: SPLEEN

value: PDX

tag: cell type


title: AML#31 cells from P1-PDX


title: M1

value: lung

value: WT

tag: treatment


title: FMRP-cTag CLIP, CA1, Control, 5 minutes, replicate 3

description: Library name: FMRP_CLIP_Control_5min_rep3

tag: cell line


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-B04

description:
Library name: DSP-1010707202201-E-B04
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: HS


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-D02

description:
Library name: DSP-1010707202201-E-D02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: CMJ


title: C1

tag: genotype


title: C2

tag: strain


title: FMRP-cTag CLIP, CA1, Control, 5 minutes, replicate 2

description: Library name: FMRP_CLIP_Control_5min_rep2

value: CA1 hippocampus


title: FMRP-cTag CLIP, CA1, Control, 5 minutes, replicate 1

description: Library name: FMRP_CLIP_Control_5min_rep1

value: Camk2a-Cre x Fmr1 cTag


title: synuclein_12wk_3

city: Suita

first: Kit-yeng

last: Sheng

address: Yamadaoka 2-2

institute: Osaka University

data_processing:
Illumina NovaSeq 6000 platform in 101-base single-end mode
Sequence mapped using TopHat software (v 2.0.13) combined with Bowtie2 (v 2.2.3) and SAM tools (v 0.1.19).
FPKM calculated using Cufflinks software (v 2.2.1)
Genome_build: mm 10
Supplementary_files_format_and_content: count, fpkm

source_name: midbrain

extract_protocol:
midbrain area containing dopaminergic neurons indicated by hKO1(+) neurons were micro-dissected and collected by FACS, directly into TRIzol LS. Total RNA extracted using Direct-zol RNA microprep kit (Zymo Research) and eluted in 8uL.
Library preparation was prepared using SMARTer Ultra-Low RNA Kit (Clontech) and cDNA amplified according to manufacturer's protocol.

treatment_protocol: bi-lateral intra-nigral injection of saline or G51D pre-formed alpha-synuclein fibrils (20 ug at 5 ug/uL)

value: neural cells

value: synuclein

tag: treatment duration

value: 12 weeks


title: FMRP-cTag CLIP, CA1, Opto, 5 minutes, replicate 4

description: Library name: FMRP_CLIP_Opto_5min_rep4

value: N/A- new files


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-B03

description:
Library name: DSP-1010707202201-E-B03
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#30 cells from P3-PDX


title: AML#30 cells from P2-PDX


title: FMRP-cTag CLIP, CA1, Opto, 5 minutes, replicate 3

description: Library name: FMRP_CLIP_Opto_5min_rep3


title: Rat_Kidney_HS_C_DSP-1010707202201-E-E07

description:
Library name: DSP-1010707202201-E-E07
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: C


title: AML#30 cells from P1-PDX


title: synuclein_12wk_2


title: Rat_Kidney_HS_CMJ_DSP-1010707202201-E-B02

description:
Library name: DSP-1010707202201-E-B02
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: synuclein_12wk_1


title: FMRP-cTag CLIP, CA1, Opto, 5 minutes, replicate 1

description: Library name: FMRP_CLIP_Opto_5min_rep1


title: saline_12wk_2

value: saline


title: saline_12wk_3


title: AML#30 cells from P0-PDX


title: Rat_Kidney_HS_C_DSP-1010707202201-E-E05

description:
Library name: DSP-1010707202201-E-E05
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#19 cells from P2-PDX


title: FMRP-cTag CLIP, CA1, Opto, 5 minutes, replicate 2

description: Library name: FMRP_CLIP_Opto_5min_rep2


title: saline_12wk_1


title: AML#30 cells from patient

value: BM

value: Patient


title: Rat_Kidney_HS_C_DSP-1010707202201-E-E06

description:
Library name: DSP-1010707202201-E-E06
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: Kidney


title: Control

city: shanghai

first: yan

last: fang

address: dongchuan Street 800

institute: shanghai jiaotong university

description: Library name: Sample7

data_processing:
CLC Genomics Workbench y11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomicbenchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 lengthfraction: 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomicbenchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: csv fles include FPK values for all Samples

growth_protocol: A2780 mesenchymal cells were maintained in 1640 supplemented with 10%fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was usedfor the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols.

treatment_protocol: LIN28B siRNA (siRNA/DSSP@lip-PEG-FA) to specifically inhibit LIN28B function. Combined with the PARP inhibitor BMN673

value: Tumor


title: Rat_Kidney_HS_C_DSP-1010707202201-E-D10

description:
Library name: DSP-1010707202201-E-D10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#17 cells from P2-PDX

value: PDX

value: Primary AML blasts


title: BMN673-2

description: Library name: Sample6


title: Rat_Kidney_HS_C_DSP-1010707202201-E-D09

description:
Library name: DSP-1010707202201-E-D09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: synuclein_7wk_3

value: 7 weeks


title: Control-2

description: Library name: Sample8


title: AML#11 cells from P2-PDX

value: SPLEEN


title: synuclein_7wk_2


title: BMN673

description: Library name: Sample4


title: synuclein_7wk_1


title: Rat_Kidney_HS_C_DSP-1010707202201-E-D08

description:
Library name: DSP-1010707202201-E-D08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring

value: HS


title: Blastoid_EnAo_day4

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

description: Single Cell FULL-LENGTH

data_processing:
10× Genomics single-cell data were pre-processed using the Cell Ranger pipeline (v.4.0.0) with default parameters.
Integration, Dimensionality reduction,clusering and visualization were done by Seurat (v.4.4.0)
Assembly: hg38
Supplementary files format and content: tsv files of cell barcodes and features. mtx files of UMI matrix

source_name: 3D co-culture blastoid and endometrial assembloids

extract_protocol:
10× genomics scRNA-seq protocol
10× genomics scRNA-seq protocol


title: Blastoid

description: Single Cell FULL-LENGTH

source_name: blastoid

value: blastoid


title: siLIN28B-2

description: Library name: Sample5


title: saline_7wk_3


title: siLIN28B

description: Library name: Sample3


title: siLIN28B+BMN673

description: Library name: Sample 1


title: Rat_Kidney_HS_C_DSP-1010707202201-E-B09

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

institute: INEM

description:
Library name: DSP-1010707202201-E-B09
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: EnAo

description: Single Cell 3' v3

source_name: endometrial assembloids

value: endometrial assembloids


title: saline_7wk_2

value: neural cells


title: Rat_Kidney_HS_C_DSP-1010707202201-E-B10

description:
Library name: DSP-1010707202201-E-B10
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: AML#11 cells from patient


title: siLIN28B+BMN673-2

description: Library name: Sample 2


title: saline_7wk_1


title: Rat_Kidney_HS_C_DSP-1010707202201-E-B08

description:
Library name: DSP-1010707202201-E-B08
Spatial transcriptomic profiling usins DSP GeoMX Nanostring


title: sci-RNA-seq3_Arabidopsis_Day5_to_Day8_Biological_Replicate_2_Technical_Replicate_1

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_Day5_to_Day8_Biological_Replicate_2_Technical_Replicate_1
sci-RNA-seq3

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

value: leaf

tag: age

value: mature rosttes


title: 22149XR-03-105

status: Public on Apr 08 2026

city: Villanova

first: Susan

last: Margulies

address: 805 Stoke Road

institute: Emory University

description:
Library name: G1HA121114U-1
Count

data_processing:
Libraries were sequenced on NovaseqX plus platform (Illumina, San Diego, CA, USA) with data yield at 40M reads in PE150 format.
The raw reads were trimmed using Trimmomatic v0.39 to remove Illumina adapters and any reads with length less than 18 bp per usual miRdeep2 requirements. Then cleaned using cutadapt v.1.9.1  which removed the commonly known miRNA specific adapter sequence, AGATCGGAAG .
Reads were mapped using the miRdeep2 mapping script within miRDeep2.pl against MiRBase and mature miRNAs for Sus scrofa (ss11.1) .
miRNAs with less than 10 counts in 50 samples were filtered out to remove noise. Outliers were detected and removed using mahalanobis outlier detection and multivariate outlier detection package in R
Assembly: ss11.1
Supplementary files format and content: txt file includes all raw counts for all samples (.txt format)

molecule: cytoplasmic RNA

organism: Sus scrofa

source_name: brain

extract_protocol:
Small RNA was isolated using the Mag-Bind® FFPE RNA 96 Kit (Omega Bio-tek Inc, Norcross, GA, USA), by following the manufacturer’s protocol. RNA concentration and purity were measured using AccuBlue® Broad Range RNA Quantitation assay (Biotium, Fremont, CA, USA) and Agilent high sensitivity Screentape (Agilent Technologies, Santa Clara, CA, USA).
cDNA libraries were constructed from 1ug of total RNA using QIAseq miRNA Library Preparation Kit (Qiagen 331502, Hilden, Germany). Libraries were measured by the Qubit 2.0 fluorometric quantitation (Thermo Fisher Scientific, Waltham, MA, USA), qPCR, and size distributions were determined by the Agilent Tapestation (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Piglets were treated with 20mg/kg/day dose of CsA intravenously via an ambulatory wireless programmable infusion pump, delivering a loading dose at 6 hour post-injury, followed by continuous infusion for 24 hours, thereby making up 30 hours of survival post-injury.

value: brain

tag: brain region

value: hippocampus + amygdala

tag: group name

value: Injured CsA treated

tag: survival time_post-injury

value: 30 hours

tag: Sex

value: female

value: Cyclosporine A treated


title: 22149XR-03-98

description:
Library name: G1HA121214U-2
Count


title: 22149XR-03-93

description:
Library name: G1HA111028U-2
Count


title: 22149XR-03-40

description:
Library name: G1HA111123U-1
Count


title: 22149XR-03-30

description:
Library name: G1HA111116U-1
Count


title: 22149XR-03-66

description:
Library name: G1HA111209U-1
Count


title: 22149XR-03-54

description:
Library name: G1HA111026U-1
Count


title: 22149XR-03-48

description:
Library name: G1FA111116U-1
Count

value: frontal lobe


title: 22149XR-03-33

description:
Library name: G1FA121128U-2
Count


title: 22149XR-03-20

description:
Library name: G1FA121214U-1
Count


title: 22149XR-03-25

description:
Library name: G1FA121214U-2
Count


title: 22149XR-03-27

description:
Library name: G1HA121214U-1
Count


title: 22149XR-03-36

description:
Library name: G1FA121114U-1
Count


title: 22149XR-03-63

description:
Library name: G3HA150717U-1
Count

value: Injured 1 week

value: 6 - 8 days

value: untreated


title: 22149XR-03-88

description:
Library name: G3HA170721U-1
Count


title: 22149XR-03-05

description:
Library name: G1HA130111U-2
Count


title: 22149XR-03-91

description:
Library name: G3HA101222-2
Count


title: 22149XR-03-15

description:
Library name: G1HA121128U-2
Count


title: 22149XR-03-79

description:
Library name: G3HA150717U-2
Count


title: 22149XR-03-78

description:
Library name: G1FA111028U-2
Count


title: 22149XR-03-53

description:
Library name: G1FA130111U-2
Count


title: 22149XR-03-100

description:
Library name: G3HA110112-1
Count


title: 22149XR-03-43

description:
Library name: G1FA111026U-1
Count


title: 22149XR-03-24

description:
Library name: G1FA111209U-1
Count


title: 22149XR-03-89

description:
Library name: G3HA140730U-2
Count


title: 22149XR-03-61

description:
Library name: G3HA140808U-1
Count


title: 22149XR-03-58

description:
Library name: G3HA140501U-2
Count


title: 22149XR-03-55

description:
Library name: G3HA110112-2
Count


title: 22149XR-03-50

description:
Library name: G3HA140501U-1
Count


title: 22149XR-03-12

description:
Library name: G3HA110126-1
Count


title: 22149XR-03-09

description:
Library name: G3HA101222-3
Count


title: 22149XR-03-45

description:
Library name: G3HA110126-3
Count


title: 22149XR-03-03

description:
Library name: G3HA140730U-1
Count


title: 22149XR-03-23

description:
Library name: G3HA140808U-2
Count


title: 22149XR-03-97

description:
Library name: G3FA140501U-2
Count


title: 22149XR-03-86

description:
Library name: G3FA150717U-2
Count


title: 22149XR-03-77

description:
Library name: G3FA150717U-1
Count


title: 22149XR-03-85

description:
Library name: G3FA140808U-1
Count


title: 22149XR-03-104

description:
Library name: G3FA110126-3
Count


title: 22149XR-03-67

description:
Library name: G3FA170721U-1
Count


title: 22149XR-03-68

description:
Library name: G3FA140730U-2
Count


title: 22149XR-03-26

description:
Library name: G3FA101222-2
Count


title: 22149XR-03-22

description:
Library name: G3FA140730U-1
Count


title: 22149XR-03-14

description:
Library name: G3FA110112-1
Count


title: 22149XR-03-99

description:
Library name: G2HA130116U-2
Count

value: Injured 1 day

value: 1 day


title: 22149XR-03-82

description:
Library name: G2HA111130U-1
Count


title: 22149XR-03-81

description:
Library name: G2HA121128U-1
Count


title: 22149XR-03-10

description:
Library name: G3FA101222-3
Count


title: 22149XR-03-72

description:
Library name: G2HA130109U-2
Count


title: 22149XR-03-74

description:
Library name: G2HA111104U-1
Count


title: 22149XR-03-71

description:
Library name: G3FA140808U-2
Count


title: 22149XR-03-13

description:
Library name: G3FA110126-1
Count


title: 22149XR-03-65

description:
Library name: G2HA111111U-1
Count


title: 22149XR-03-41

description:
Library name: G3FA110112-2
Count


title: 22149XR-03-44

description:
Library name: G2HA121219U-2
Count


title: 22149XR-03-96

description:
Library name: G2FA111130U-1
Count


title: 22149XR-03-37

description:
Library name: G2HA111118U-1
Count


title: 22149XR-03-06

description:
Library name: G2HA111026U-2
Count


title: 22149XR-03-62

description:
Library name: G2FA111118U-1
Count


title: 22149XR-03-94

description:
Library name: G3FA140501U-1
Count


title: 22149XR-03-73

description:
Library name: G2FA121219U-2
Count


title: 22149XR-03-51

description:
Library name: G2FA111026U-2
Count


title: 22149XR-03-39

description:
Library name: G2HA130118U-1
Count


title: 22149XR-03-92

description:
Library name: G2FA130116U-2
Count


title: 22149XR-03-84

description:
Library name: G2FA121128U-1
Count


title: 22149XR-03-04

description:
Library name: G2FA111104U-1
Count


title: 22149XR-03-64

description:
Library name: G2FA111111U-1
Count


title: 22149XR-03-101

description:
Library name: G4HA160427U-1
Count

value: Sham/Naïve

value: 0 - 8 days


title: 22149XR-03-95

description:
Library name: G4HA140529U-1
Count


title: 22149XR-03-80

description:
Library name: G4HA160513U
Count


title: 22149XR-03-69

description:
Library name: G4HA130603I-2
Count


title: 22149XR-03-83

description:
Library name: G4HA110513-2
Count


title: 22149XR-03-70

description:
Library name: G4HA120604F-2
Count


title: 22149XR-03-02

description:
Library name: G2FA130118U-1
Count


title: 22149XR-03-31

description:
Library name: G2FA130109U-2
Count


title: 22149XR-03-60

description:
Library name: G4HA110606-2
Count


title: 22149XR-03-75

description:
Library name: G4HA110112-3
Count


title: 22149XR-03-103

description:
Library name: G4HA140515U-3
Count


title: 22149XR-03-59

description:
Library name: G4HA160429U
Count


title: 22149XR-03-76

description:
Library name: G4HA130603I-3
Count


title: 22149XR-03-29

description:
Library name: G4HA120514F-2
Count


title: 22149XR-03-32

description:
Library name: G4HA110831B
Count


title: 22149XR-03-18

description:
Library name: G4HA140522U
Count


title: 22149XR-03-35

description:
Library name: G4HA101222-1
Count


title: 22149XR-03-19

description:
Library name: G4HA110902B
Count


title: 22149XR-03-52

description:
Library name: G4FA110902B
Count


title: 22149XR-03-90

description:
Library name: G4FA160427U-1
Count


title: 22149XR-03-47

description:
Library name: G4FA110112-3
Count


title: 22149XR-03-49

description:
Library name: G4FA140515U-3
Count


title: 22149XR-03-46

description:
Library name: G4FA140522U
Count


title: 22149XR-03-106

description:
Library name: G4FA130610I-3
Count


title: 22149XR-03-34

description:
Library name: G4FA110513-2
Count


title: 22149XR-03-87

description:
Library name: G4FA110831B
Count


title: 22149XR-03-57

description:
Library name: G4FA101222-1
Count


title: 22149XR-03-56

description:
Library name: G4HA130610I-3
Count


title: 22149XR-03-38

description:
Library name: G4FA130603I-3
Count


title: kidney organoids protocol suspension

city: Melbourne

first: Maria Rosaria

last: Nucera

state: VICTORIA

address: 50, Flemington road

department: Paediatrics

country: Australia

institute: University of Melbourne

description:
Library name: kidney_organoids_sus
organoid model
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the SAW pipeline
Images in format .czi were converted into .ipr and .tar format using ImageStudio software.
Assembly: mm10 for mouse tissue and GRCh38 for human organoids
Supplementary files format and content: file.gef : output of SAW pipeline
Supplementary files format and content: anndata.h5ad : output of SAW pipeline
Supplementary files format and content: image.ipr : image converted using ImageStudio, input of SAW pipeline
Supplementary files format and content: image.tar : image converted using ImageStudio, input of SAW pipeline
Library strategy: Spatial Transcriptomics

source_name: kidney organoids

extract_protocol:
Samples were prepared and processed using the STOmics Transcriptomics kit (STOmics Cat# 111KT114) in accordance with manufacturer’s instructions (BGI Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B) with slight variations.
The cDNA purification and library preparation of each sample was constructed using the STOmics library preparation kit (STOmics Cat# 111KL114) in accordance with manufacturer’s instructions (BGI STOmics Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B).

treatment_protocol: the tissues are fresh frozen

value: kidney organoids


title: blood organoids

description:
Library name: blood_organoids
organoid model
Fresh frozen Spatial transcriptome sequencing

source_name: blood organoids

value: blood organoids


title: 22149XR-03-21

description:
Library name: G4FA130603I-2
Count


title: valve organoids

description:
Library name: valve_organoids
organoid model
Fresh frozen Spatial transcriptome sequencing

source_name: valve organoids

value: valve organoids


title: 22149XR-03-11

description:
Library name: G4FA160513U
Count

value: brain


title: 22149XR-03-16

description:
Library name: G4FA120514F-2
Count


title: 22149XR-03-07

description:
Library name: G4FA110126-2
Count


title: 22149XR-03-28

description:
Library name: G4FA160429U
Count


title: AMA2

city: Guangzhou

first: shuyi

last: kuang

state: Guangdong

address: ShaTai southern load

institute: Southern Medical Univercity

description: Library name: Sample5

data_processing:
FASTQ was used to remove adapter contamination and filter low-quality reads to obtain clean data. Single-cell transcriptome analysis was performed using UMI-tools to identify the cell barcode whitelists. Using the STAR map of custom parameters in the UMI-tools standard pipeline, UMI-based clean data were mapped to the human genome (Ensemble version 104) to obtain UMIs counts for each sample.
Assembly: The human genome (Ensemble version 104)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Placenta

extract_protocol:
Fresh placental samples were macroscopically dissected from the central region of the maternal-facing surface to separate the decidual and trophoblast layers. The decidual layers were cut into small pieces and digested with 1 mg/mL collagenase type IV and 200 U/mL DNase I in Roswell Park Memorial Institute (RPMI)-1640 medium for 2–3 h at 37 °C. Thereafter, red blood cells (RBCs) were removed from the suspensions and filtered through a 70 μm cell filter. Decidual mononuclear cells were isolated using 40/80% Percoll density gradient centrifugation.
Library was performed according to the manufactor's instruments (BD Rhapsody).

value: Placenta

value: human

value: decidual LOX1+ immune cells

value: Pregnancies with AMA


title: AMA1

description: Library name: Sample4


title: heart organoids

description:
Library name: heart_organoids
organoid model
Fresh frozen Spatial transcriptome sequencing

source_name: heart organoids

value: heart organoids


title: L. lactis subps. cremoris MG1363_penicillin_rep2

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Life sciences center

country: Lithuania

institute: Vilnius Universitye

description: Library name: Sample 6

data_processing:
Read quality was evaluated using FASTQC (v0.11.9). UMI work was performed using UMI-tools (1.1.6). Quality trimming and filtering was performed using cutadapt (4.4) and seqPurge (2022_12).
Cleaned reads were mapped to the reference gemome using hisat2 (2.2.1) and deduplicated using UMI_tools (1.1.6)
Reads were quantified using featureCounts (2.0.6). sRNAs were predicted using APERO and an in-house R script.
Assembly: NC_009004.1
Supplementary files format and content: TXT format files with gene identificator and gene coverage.

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: bacteria

growth_protocol: Lactococcus lactis subsp. cremoris MG1363 was cultivated at 30°C in BD™ Difco™ M17 broth supplemented with 0.5% glucose (GM17). Overnight cultures were used to inoculate fresh GM17 medium at an initial OD600 of 0.1 and grown until the selected growth stage.

extract_protocol:
Bacteria were mixed with 1/8 volume of ice-cold STOP solution (95% ethanol and 5% acid phenol) and centrifuged at 1,800 × g for 20 min at 4°C. Cells were ground to a fine powder using liquid nitrogen and total RNA was extracted with RNAzolRT (RN 190) (Molecular Research Center, Inc.). 50–500 nt RNA was cut out of 8% denaturing PAA gel.
50–500 nt RNA was treated with DNase I, RNase free (Thermo Scientific) and recovered from the reaction using RNA Clean & Concentrator-5 Kit (Zymo Research). 5S rRNA was depleted using the modified RiboMinus Transcriptome Isolation Kit, bacteria (Invitrogen) where 4 μl of 100 μM mix of three probes specific to L. lactis 5S rRNA were used. After ethanol precipitation RNA was treated with RNA 5′ Pyrophosphohydrolase (RppH) (New England Biolabs), recovered with RNA Clean & Concentrator-5 Kit and 165 ng were taken for further processing using NEXTflex Small RNA-Seq Kit v3 (PerkinElmer) with following modifications: at Step E, incubation at 42°C was extended to 60 min; at Step G, 16 PCR cycles were performed; and Steps F and H1 were carried out as described in alternative protocol for Preparing Libraries without Size Selection.

treatment_protocol: For the five-point library, the biomass was collected at OD600 0.2, 0.8, 1.9, 3.0, and 3.3. For treated libraries, bacteria were grown until they reached an OD600 of 0.5. At this point, PnG or Lys was added to a final concentration of 0.125 µg/ml and 0.5 mg/ml, respectively. Bacteria were further grown to the mid-exponential phase (OD600 of 1.6-1.8).

value: bacteria


title: lung organoids

description:
Library name: lung_organoids
organoid model
Fresh frozen Spatial transcriptome sequencing

source_name: lung organoids

value: lung organoids


title: L. lactis subps. cremoris MG1363_five growth points

description: Library name: Sample 7


title: cartilage organoid

description:
Library name: cartilage_organoids
organoid model
Fresh frozen Spatial transcriptome sequencing

source_name: cartilage organoid

value: cartilage organoid


title: 22149XR-03-01

description:
Library name: G4FA120604F-2
Count

value: frontal lobe

value: female

value: untreated


title: 22149XR-03-17

description:
Library name: G4HA110126-2
Count

value: hippocampus + amygdala

value: Sham/Naïve


title: 22149XR-03-08

description:
Library name: G4FA140529U-1
Count

value: 0 - 8 days


title: HP3_EVT

description: Library name: Sample14

data_processing:
The R package DESeq2 (1.44.0) was used for diferential analysis of the count data and R package clusterProfiler (4.12.6) was used to perform different genes enrichment analysis.
Assembly: GRCh38.p13
Supplementary files format and content: csv files include FPKM values for each sample

extract_protocol:
Cells were extracted for RNA by Trizol reagent and subsequently sequenced using the DNBSEQ platform
RNA libraries were prepared for sequencing using standard DNBSEQ platform protocols

value: Extravillus trophoblasts

value: Healthy pregancy group


title: 22149XR-03-42

description:
Library name: G4FA110606-2
Count

value: brain


title: HP2

description: Library name: Sample2

value: Placenta

value: Healthy pregancies


title: HP3

description: Library name: Sample3

value: human

value: decidual LOX1+ immune cells


title: L. lactis subps. cremoris MG1363_control_rep2

description: Library name: Sample 2


title: L. lactis subps. cremoris MG1363_lysozyme_rep1

description: Library name: Sample 3


title: HP2_EVT

description: Library name: Sample13


title: L. lactis subps. cremoris MG1363_control_rep1

description: Library name: Sample 1


title: L. lactis subps. cremoris MG1363_penicillin_rep1

description: Library name: Sample 5


title: HP1_EVT

description: Library name: Sample12


title: HP1

description: Library name: Sample1


title: HP_PL_4

description: Library name: Sample11

value: decidual PMN-MDSCs


title: L. lactis subps. cremoris MG1363_lysozyme_rep2

description: Library name: Sample 4

value: bacteria


title: HP_PL_3

description: Library name: Sample10


title: Donor 2, Cas9EDV Day 0, sample collection Day1

city: San Francisco

first: Pascal

last: Devant

address: 1650 Owens Street

institute: Gladstone Institutes

description: Library name: Count_11EDV-AAV-D1-d2.counts

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCh38
Supplementary files format and content: processed data format:csv, processed data content: raw counts

source_name: Peripheral blood

growth_protocol: Primary human monocytes were isolated from fresh peripheral blood Leukopaks (STEMCELL Technologies) with institutional review board-approved informed written consent. Leukopaks were washed twice with EasySep buffer (sterile PBS pH 7.4, 2% FCS, 1 mM EDTA pH 8.0) before isolation of monocytes using the Human Monocyte Enrichment kit without CD16 depletion (STEMCELL Technologies; 100-1525) according to manufacturer’s instruction. Briefly, PBMCs were diluted to 100x106 cells/ml in EasySep buffer, mixed with 100 µl of antibody cocktail per 100 million cells and incubated at RT for 5-10 mins. Magnetic beads were added and following 3 min of incubation at RT, tubes containing cells were placed in a magnetic field for 10 mins. Unbound cells (pure monocyte fraction) were removed, washed one more time with EasySep buffer. Cells were then counted and resuspended in Immunocult SF Macrophage media (STEMCELL technology; 10961) at a density of 1x106 cells/ml and seeded in TC-treated 6-well plate ( 3x106 cells per well). For macrophage differentiation, media was supplemented with 20 ng/ml of M-CSF (Peprotech; 300-25). Media was replenished every 24-72 h by adding at least one half volume of fresh media and cytokines. All tissue culture was performed under sterile conditions and cells were cultured in temperature-controlled incubators at 37°C and 5% CO2.

extract_protocol:
RNA extraction, library preparation, and next-generation sequencing was performed by GENEWIZ Inc. Total RNA was extracted from frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200(Agilent technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 ° C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’e ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Freshly isolated monocytes subjected to Cas9EDV-mediated gene editing (50 ul of concentrated EDV per well) or nucleofection with Cas9-RNP targeting the AAVS1 locus, following by culture in M-CSF-containing media. Cells were harvested on Day 1 or Day 7 post isolation. Cells were detached using Accutase, washed twice with DPBS, pelleted by centrifugation.

value: Peripheral blood

value: monocyte-derived macrophages

tag: donor

value: Donor 2

value: Cas9EDV Day 0, sample collection Day1


title: Donor 2, nucleofection Day 0, sample collection Day7

description: Library name: Count_13Nuc-AAV-D7-d2.counts


title: Donor 2, untreated, sample collection Day7

description: Library name: Count_12NTD-D7-d2.counts

value: untreated, sample collection Day7


title: Donor 2, Cas9EDV Day 0, sample collection Day7

description: Library name: Count_14EDV-AAV-D7-d2.counts

value: Cas9EDV Day 0, sample collection Day7


title: HP_PL_2

description: Library name: Sample9


title: HP_PL_1

description: Library name: Sample8


title: Donor 2, nucleofection Day 0, sample collection Day1

description: Library name: Count_10Nuc-AAV-D1-d2.counts


title: HP_PB_4

description: Library name: Sample7

value: peripheral PMN-MDSCs


title: Donor 2, Cas9EDV Day 4, sample collection Day7

description: Library name: Count_15EDV-AAV-D47-d2.counts

value: Cas9EDV Day 4, sample collection Day7