title: SABERb4_linB2.2-14.124.2, brain4, SABER-Seq

city: Philadelphia

first: Bushra

last: Raj

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Raw FASTQ reads were aligned against zebrafish genome, built from GRCz.109.gtf and the GRCz11.fa files, using the Cell Ranger count pipeline to generate gene-by-cell count matrices (filtered barcode matrix). The count matrices were processed using the standard workflow of the Seurat (v5.0.2) R package with modifications. Briefly, all count matrices were separately loaded into R. Seurat objects were then created with modified parameters, requiring features to be detected in at least 3 cells and cells to contain at least 300 genes. Subsequently, the Seurat objects were merged to create a single Seurat object. Cells with RNA counts between 300 and 4000 and a mitochondrial gene percentage of less than 9% were selected for downstream analysis. Gene expression values were log-normalized with the default parameters and scaled for the top 3000 variable genes. The scaled data was then used to compute the 50 principal components. Cells were iteratively clustered using the Louvain algorithm after identifying neighboring cells. Differentially expressed genes for each cluster were identified using genes that are detected in at least 10% of cells in either of the two clusters and genes showing a minimum difference of 10% between the two clusters. Cell types were annotated using known marker genes.  The SABER-seq FASTQ reads were processed using the Cell Ranger count pipeline, similar to the transcriptomic reads. A bash script was then used to generate a text file containing all FASTQ headers and error-corrected cell barcodes for SABER-seq data. After loading filtered barcode matrices into R, error-corrected cell barcodes from transcriptomic reads were isolated and matched against those in the text file to identify common cell barcode that are shared between the transcriptomic and SABER-seq datasets. The resulting text file contained redundant error-corrected cell barcodes associated with different UMIs for the same cell. Thus, unique error-corrected cell barcodes were isolated to create a text file containing unique FASTQ headers and error-corrected barcodes. Subsequently, FASTQ reads matching the FASTQ headers in this file were extracted from the SABER-seq raw reads using a Python script. SABER-seq barcodes were analyzed using the scGESTALT pipeline available on Github as described previously7,35. To analyze differences in barcode detection and editing frequencies between cell types a binomial test was used.
scRNA-seq data was analyzed using the following protocol. Raw FASTQ reads were aligned against zebrafish genome, built from GRCz.109.gtf and the GRCz11.fa files, using the Cell Ranger count pipeline to generate gene-by-cell count matrices (filtered barcode matrix). The count matrices were processed using the standard workflow of the Seurat (v5.0.2) R package with modifications. Briefly, all count matrices were separately loaded into R. Seurat objects were then created with modified parameters, requiring features to be detected in at least 3 cells and cells to contain at least 300 genes. Subsequently, the Seurat objects were merged to create a single Seurat object. Cells with RNA counts between 300 and 4000 and a mitochondrial gene percentage of less than 9% were selected for downstream analysis. Gene expression values were log-normalized with the default parameters and scaled for the top 3000 variable genes. The scaled data was then used to compute the 50 principal components. Cells were iteratively clustered using the Louvain algorithm after identifying neighboring cells. Differentially expressed genes for each cluster were identified using genes that are detected in at least 10% of cells in either of the two clusters and genes showing a minimum difference of 10% between the two clusters. Cell types were annotated using known marker genes. Finally, the data was visualized using UMAP.
SABER-seq barcode analysis was performed using the following protocol. The SABER-seq FASTQ reads were processed using the Cell Ranger count pipeline.A bash script was then used to generate a text file containing all FASTQ headers and error-corrected cell barcodes for SABER-seq data. Error-corrected cell barcodes from transcriptomic reads were isolated and matched against those in the text file to identify common cell barcode that are shared between the transcriptomic and SABER-seq datasets. The resulting text file contained redundant error corrected cell barcodes associated with different UMIs for the same cell. Thus, unique error corrected cell barcodes were isolated to create a text file containing unique FASTQ headers and error-corrected barcodes. Subsequently, FASTQ reads matching the FASTQ headers in this file were extracted from the SABER-seq raw reads using a Python script. SABER-seq barcodes were analyzed using the scGESTALT pipeline available on Github as described previously. To analyze differences in barcode detection and editing frequencies between cell types a binomial test was used.
Assembly: GRCz11
Supplementary files format and content: *.h5 files contain fileted features/genes and barcode data generated from cell ranger pipeline.
Supplementary files format and content: LinC1_Filtered_Fastq_Headers_CB.txt,LinC2_Filtered_Fastq_Headers_CB.txt,LinD1_Filtered_Fastq_Headers_CB.txt,LinD2_Filtered_Fastq_Headers_CB.txt,LinD3_Filtered_Fastq_Headers_CB.txt files contain filtered and unique fastq headers and cell barcodes after matching the trasncriptomic cell barcodes.
Supplementary files format and content: SABERb1_linC1_S4_BrainC1_S6.CB.xlsx,SABERb1_linC2_S5_BrainC2_S7.CB.xlsx,SABERb2_linD1_S1_BrainD1_S8.CB.xlsx,SABERb2_linD2_S2_BrainD2_S9.CB.xlsx,SABERb2_linD3_S3_BrainD3_S10.CB.xlsx,SABERb4_linB2.1-13.123.2.With.Primer.stats.xlsx,SABERb4_linB2.2-14.124.2.With.Primer.stats.xlsx files contain the SABER-Seq output after matching reads to the reference sequence.

organism: Danio rerio

source_name: zebrafish whole brain

growth_protocol: This work was performed under protocol numbers 807110 and 807259, which were approved by the University of Pennsylvania’s Office of Animal Welfare of Institutional Animal Care and Use Committee (IACUC). All zebrafish work in this study follows the University of Pennsylvania Institutional Animal Care and Use Committee regulations.

extract_protocol:
Wild type and SABER x her4.3:switchCas9 zebrafish brains were harvested and dissociated at 21-23 dpf as described previously with the following modifications. All microcentrifuge tubes were treated with 1% BSA/DPBS overnight to prevent cell loss due to adhesion. Brains were dissociated with 1 mL of 20 units/ml papain in EBSS media and incubated at 37 °C for 20 min. Cells were resuspended with ~150 μl ice cold 1%BSA/DPBS solution.
Transcriptome libraries were processed according to the manufacturer’s instructions (Single Cell 3’ v3 kit). Transcriptome libraries were sequenced using HiSeq S4 300 cycle kits (Novogene) and Novaseq SP 100 and 200 cycle kits (MedGenome). To generate SABER-seq libraries, samples post cDNA amplification and prior to fragmentation were split into two parts. One part was processed for transcriptome libraries as instructed by the manufacturer. The other part was processed for SABER-seq libraries as follows. To enrich for SABER barcodes, 5 µl of the whole transcriptome cDNA was PCR amplified with 10X_p140v1UP  (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT CGTCGTAGATCTTCATCGTGATG) and 10XPCR1F (CTACACGACGCTCTTCCGATCT) primers and Q5 polymerase. The reaction conditions were: 98 °C, 30 s; [98 °C, 10 s; 68 °C, 25 s; 72 °C, 15 s] x 14 cycles; 72 °C, 2 min. The reaction was cleaned up with 0.8X SPRISelect beads and eluted in 20 µl elution buffer (EB) buffer. A second PCR was carried out using 3 µl of PCR1 product and 10XPCR1F and 10X_p140v2Sa (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT GAAACTACATGGGGTcaGCTC) primers. Reaction conditions were same as PCR1 except only 13 cycles were completed. At this point, 2 different clean up conditions were used: iteration 1 (SABER-seq_v0) and iteration 2 (SABER-seq_v1). For iteration 1, the reaction was cleaned up with 0.8X SPRISelect beads and eluted in 20 µl elution buffer (EB) buffer similar to PCR1.  For iteration 2, an optimization was trialed, and the reaction was cleaned up with right side size selection using SPRIselect beads (0.6X beads used initially and supernatant was rebound with 1.5X beads). The product was eluted in 20 µl EB. Finally, adapters and sample indices were incorporated in a third PCR reaction using 5-7 µl of a 1:10 dilution of PCR2 product. Reactions conditions were same as PCR1 except 9-10 cycles were completed. Primers used: 10XP5Dual_Hx (AATGATACGGCGACCACCGAGATCTACAC-xxxxxxx xxx-ACACTCTTTCCCTACACGACGCTCTTCCGATCT), 10XP7Dual_H5 (AATGATACGGCGAC CACCGAGATCTACAC-xxxxxxxxxx-ACACTCTTTCCCTACACGACGCTCTTCCGATCT), where x represents index bases from the 10X Dual Index Kit TT, SetA H index entries. For iteration 1, the third PCR reaction was cleaned up with 0.8X SPRISelect beads and eluted in 20 µl elution buffer (EB) to generate final libraries. For iteration 2, the third PCR reaction was cleaned up with right side size selection using SPRIselect beads (0.65X beads used initially and supernatant was rebound with 1.5X beads). SABER-seq libraries were sequenced using Novaseq SP 200 cycle kits (MedGenome) with 5-10% PhiX spike-in. Sequencing parameters: Read1 28 cycles, Read2 151 cycles, Index1 10 cycles, Index2 10 cycles. Standard sequencing primers were used.

value: zebrafish whole brain

value: 21-23 dpf, Juvenile

value: WT/TLAB


title: NOVA1-CLIP, hu/hu, P21, cortex, rep1

status: Public on Dec 11 2024

type: SRA

city: NY

first: Yoko

last: Tajima

state: New York

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: transcriptomic

data_processing:
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping on mm10)
collapsing of PCR duplicates
clustering of unique reads
Assembly: mm10
Supplementary files format and content: bedgraph

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Brain tissue was UV irradiated and subjected to NOVA1-CLIP
Partial RNAse digestion, RNA linker ligation and PCR amplification. NOVA1 bound fragments were ligated to a degenerate 5'linker and a 3'linker.

tag: strain background

tag: tissue

value: brain

tag: tissue compartment

value: cortex

tag: genotype

tag: developmental stage


title: SABERb4_linB2.1-13.123.2, brain4, SABER-Seq

state: PA

description: 10X Genomics

library_source: transcriptomic single cell


title: media_sham_6h_exp2_2

type: RNA

city: Bethesda

first: Simone

last: Grant

state: MD

address: 4301 Jones Bridge Rd

department: PHA

institute: Uniformed Services University

scan_protocol: Evaluation of the expression of 798 unique miRNAs was evaluated with the nCounter MAX/FLEX Analysis System using the Nanostring nCounter® Human v3 miRNA Expression Panels (NanoString Technologies, Seattle, WA, USA). Samples were prepared and ran according to the manufacturer’s instructions to determine the mean copy of each miRNA probe of interest.  Housekeeping genes for normalization included: ribosomal protein L10, beta-actin, beta-2-microglobulin, glyceraldehyde 3-phosphate dehydrogenase, and ribosomal protein L19, as well as endogenous miRNAs and positive and negative controls. Raw data was analyzed by nSolver Software version 4.0 (NanoString Technologies).

data_processing: All samples passed quality control checks and  normalization was carried out using the geometric mean of the ligation factors. miRNA expression differences in sham and impact injury at the different time points were measured using t-tests, with the Benjamini-Hochberg’s False Discovery Rate (FDR) method for multiple comparison corrections. Expression data were log2 transformed for presentation.

label: not provided

organism: Homo sapiens

source_name: Scaffold Triculture Media

growth_protocol: 3D human tricultures were fabricated following an earlier published protocol (6, 7). Human induced neural stem cell (hiNSCs)  , human primary astrocytes (Sciencell research laboratories, cat. no. 1800), and HMC3 (human microglial) cells were allowed to reach nearly 100% confluency at the day of triculture seeding. All cell types were collected and concentrated as described in the individual culture methods. Silk scaffolds freshly coated with poly-ornithine (PLO) (Sigma, cat.no. A004C) - and laminin  were placed in 96-well plates, and a vacuum manifold was used to remove excess liquid (45). Each scaffold was seeded with a 40L cell suspension containing 2:0.5:0.1 million neurons, astrocytes, and microglia, followed by 30 minutes of incubation at 37°C to allow cell adhesion to the scaffolds. To ensure efficient cell attachment, the freshly seeded scaffolds were submerged in 150L of Neuronal media (composed of NeuroBasal medium supplemented with 2% B-27, 1% Anti-Anti, 1% Glutamax, all from Invitrogen, and 1% astrocyte growth factors, Sciencell research laboratories) and incubated overnight in a tissue culture incubator (37°C, 5% CO2 in a humidified atmosphere). The following day, the cell-seeded scaffolds were transferred to new 96-well plates to remove the unattached cells, embedded with 100L of collagen type I solution (Corning or R&D systems, 3 mg/mL with a pH adjusted to 7.0-7.2 with NaOH), and incubated for 30 minutes at 37°C to allow the collagen gel to crosslink. Neuronal media (150L) was added to all scaffolds and incubated for 24h at 37°C. The following day, 3D tricultures were moved into 48-well plates with 1 ml of Neuronal media in each well. Half the media volume was changed every fourth day until the tissues were used for experiments (6-7 weeks).

extract_protocol: miRNA isolation and purification were performed on 1 mL of triculture media collected from sham and impact samples at 6, 24, 72 hours post-injury. Samples were immediately stored in -80 °C. Once all samples were collected, samples were thawed and miRNA purification was performed using the mirVANA miRNA isolation kit (AM1560, Ambion, Life Technologies). Briefly, miRNA homogenate additive and Acid-Phenol:Chloroform was added to the media and centrifuged at 10,000 x g for 5 minutes. The upper aqueous phase containing the RNA was then collected and transferred to a new tube. Total RNA purification followed by miRNA purification was carried out using the filter cartridges from the mirVANA miRNA isolation kit per the manufacturer’s instructions. miRNA was collected by eluting the filter cartridge with 100 μl of nuclease-free water.  miRNA samples were further concentrated for Nanostring analysis using the Oligo Clean and Concentrator Kit (D4060, Zymo Research) per the manufacturer’s instructions. The eluate, containing the miRNA was collected and the concentration was measured using the Quibit miRNA assay kit (Q32880, Molecular probes, Life Technology) per manufacturer’s instructions.

treatment_protocol: 3D brain-like tissues were placed on a flat weigh boat and subjected to contusion injury using a pneumatic cylinder with a 3 mm flat tip impactor at a velocity of 6 m/s, penetration depth 0.6 mm, and a dwell time duration of 200 ms (6). Sham tissues were handled similarly to the injured tissues but without receiving the contusion injury. Following injury or sham protocol, the tissues were incubated at 37 °C in 5% CO2 in a humidified atmosphere until the indicated time marks for imaging and/or media collection for miRNA analysis.

tag: injury

value: No injury (Sham)

tag: timepoint

value: 6 Hours Post-Injury

tag: molecule type

value: miRNA


title: L-shFgf13+HG-PA rep3

city: wenzhou

first: jia

last: sun

address: wenzhou medical university

country: China

institute: wenzhou medical university

data_processing:
HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) was used to map reads to the genome (Homo sapiens Ensembl v101)
The mapped reads of each sample were assembled using StringTie.
 Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HRGEC

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HRGEC

tag: cell type

value: Human renal glomerular endothelial cells

tag: treatment

value: HG-PA-treated Fgf13 KD HRGEC


title: CTCF_ChIP_PS_Scml2-KO_rep2

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

library_source: genomic

data_processing:
Raw sequence reads were trimmed and filtered using Sickle.
Trimmed sequence reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 version 2.4.5.
PCR duplicates reads were removed using Picard tools version 2.26.9.
To visualization of ChIP-seq using IGV, normalized genome coverage tracks based on counts per million mapped reads were generated as bigwig files using bamCoverage function of deepTools with ‘--binSize=5 --normalization CPM’ parameter.
Peaks were called using MACS version 2.2.7.1
The ngs.plot package was used to draw tag density and heat maps for read enrichment.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: testis

extract_protocol:
Germ cells were isolated from mouse testis by STA-PUT method or MACS.
Cells were fixed in 1% formaldehyde for 10 min at room temperature. Nuclei were isolated by lysis buffer. Chromatin was sonicated by Covaris sonicater and used for ChIP experiments. DNA libraries were prepared through the ChIPmentation method (PMID: 26280331).

value: testis

tag: strain

tag: age

value: adult

value: Pachyten spermatocytes

tag: chip antibody

value: CTCF


title: CTCF_ChIP_PS_Scml2-KO_rep1


title: L-shFgf13+HG-PA rep2


title: SABERb2_linD3, brain2, SABER-Seq

description: 10X Genomics


title: Whole rosette tissue, wild type, 21 day, input, ChIP, rep2

city: West Lafayette

first: Joe

last: Ogas

state: Indiana

address: 175 S. University Street

department: Department of Biochemistry

institute: Purdue University

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using Bowtie2 (v 2.2.1) in very-sensitive-end-to-end mode
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The reads of individual biological replicate were merged into one BAM file using SAMtools (v 1.17)
The BAM files of individual replicate and the merged sample were converted to paired-end BED files using BEDTools
The enriched peaks were called by using epic2 (parameters: egf = 0.85, bin = 200, g = 1, and fdr = 0.05)
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample of H2A.Z-marked genes
Supplementary files format and content: tab-delimited text file includes raw counts for each sample of H3K27me3-marked genes
Supplementary files format and content: BED files includes the genomic regions as coordinates for H3K27me3 enriched regions
Supplementary files format and content: BED files includes the genomic regions as coordinates for H2A.Z enriched regions
Supplementary files format and content: BED files includes the genomic regions as coordinates and associated annotations for overlaps between genes and H3K27me3 enriched regions
Supplementary files format and content: BED files includes the genomic regions as coordinates and associated annotations for overlaps between genes and H2A.Z enriched regions

organism: Arabidopsis thaliana

source_name: Whole Rosette tissue

growth_protocol: Plants used for ChIP-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
4 g of 21-day-old whole rosette tissue were collected for each biological replicate. Nuclear lysis buffer was replaced with 1.7 mL of ChIP Lysis Buffer (50 mM HEPES-NaOH (pH =7.4), 16.7 mM Tris-HCl (pH = 8), 1 mM EDTA (pH = 8), 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 0.1% Sodium deoxycholate, 1 cOmpleteTM mini tablet / 10 mL solution). The total chromatin samples were sonicated using Bioruptor Pico. Sheared chromatin samples were stored at -80 °C overnight prior to the immunoprecipitation. The following antibodies were used in the analysis: Anti-H3 (ab1791, Abcam) (1:200 dilution), Anti-H3K27me3 (07-449, Millipore) (1:100 dilution), and Anti-H2A.Z (1.5 µg for a 500 µL IP sample) (Deal et al., 2007). The QIAquick MinElute PCR purification kit was replaced with ChIP DNA Clean & Concentrator purification kit (D5205, Zymo research) for elution of the ChIP DNA. The eluted ChIP DNA was quantified us a Qubit 2.0 Fluorometer and used immediately in library construction.
0.5 ng eluted ChIP DNA was used for each library construction. ChIP DNA libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit (NEB; catalog no. E7645L) according to the manufacturer’s manual. Illumina Multiplexing adapter was used for indexing. Pair-ended,150-bp sequencing was performed using an Illumina Novaseq S4 lane.

value: Whole Rosette tissue

tag: ecotype

value: Wild type

tag: development stage


title: media_sham_6h_exp2_1


title: media_sham_6h_exp1_6


title: SABERb2_linD2, brain2, SABER-Seq

description: 10X Genomics

value: zebrafish whole brain


title: L-shFgf13+HG-PA rep1


title: CTCF_ChIP_PS_WT_rep2

value: wild type


title: HG-PA rep3

value: HG-PA-treated HRGEC


title: SABERb2_linD1, brain2, SABER-Seq

description: 10X Genomics

value: 21-23 dpf, Juvenile

value: WT/TLAB


title: media_sham_6h_exp1_5

value: No injury (Sham)


title: media_sham_6h_exp1_4

value: 6 Hours Post-Injury


title: HG-PA rep2


title: media_sham_6h_exp2_4

value: miRNA


title: CTCF_ChIP_THY1_WT_rep2

value: 6-8 days

value: Thy1+ spermatogonia


title: SABERb1_linC1, brain1, SABER-Seq

description: 10X Genomics


title: HG-PA rep1

value: HRGEC

value: Human renal glomerular endothelial cells


title: CTCF_ChIP_THY1_WT_rep1

value: testis


title: media_sham_6h_exp1_3


title: media_sham_6h_exp1_2


title: CTCF_ChIP_PS_WT_rep1

value: adult

value: Pachyten spermatocytes


title: SABERb4_brainB2_2, brain4, transcriptome

description:
SABERb4.2_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds

data_processing:
Raw FASTQ reads were aligned against zebrafish genome, built from GRCz.109.gtf and the GRCz11.fa files, using the Cell Ranger count pipeline to generate gene-by-cell count matrices (filtered barcode matrix). The count matrices were processed using the standard workflow of the Seurat (v5.0.2) R package with modifications. Briefly, all count matrices were separately loaded into R. Seurat objects were then created with modified parameters, requiring features to be detected in at least 3 cells and cells to contain at least 300 genes. Subsequently, the Seurat objects were merged to create a single Seurat object. Cells with RNA counts between 300 and 4000 and a mitochondrial gene percentage of less than 9% were selected for downstream analysis. Gene expression values were log-normalized with the default parameters and scaled for the top 3000 variable genes. The scaled data was then used to compute the 50 principal components. Cells were iteratively clustered using the Louvain algorithm after identifying neighboring cells. Differentially expressed genes for each cluster were identified using genes that are detected in at least 10% of cells in either of the two clusters and genes showing a minimum difference of 10% between the two clusters. Cell types were annotated using known marker genes.  The SABER-seq FASTQ reads were processed using the Cell Ranger count pipeline, similar to the transcriptomic reads. A bash script was then used to generate a text file containing all FASTQ headers and error-corrected cell barcodes for SABER-seq data. After loading filtered barcode matrices into R, error-corrected cell barcodes from transcriptomic reads were isolated and matched against those in the text file to identify common cell barcode that are shared between the transcriptomic and SABER-seq datasets. The resulting text file contained redundant error-corrected cell barcodes associated with different UMIs for the same cell. Thus, unique error-corrected cell barcodes were isolated to create a text file containing unique FASTQ headers and error-corrected barcodes. Subsequently, FASTQ reads matching the FASTQ headers in this file were extracted from the SABER-seq raw reads using a Python script. SABER-seq barcodes were analyzed using the scGESTALT pipeline available on Github as described previously7,35. To analyze differences in barcode detection and editing frequencies between cell types a binomial test was used.
scRNA-seq data was analyzed using the following protocol. Raw FASTQ reads were aligned against zebrafish genome, built from GRCz.109.gtf and the GRCz11.fa files, using the Cell Ranger count pipeline to generate gene-by-cell count matrices (filtered barcode matrix). The count matrices were processed using the standard workflow of the Seurat (v5.0.2) R package with modifications. Briefly, all count matrices were separately loaded into R. Seurat objects were then created with modified parameters, requiring features to be detected in at least 3 cells and cells to contain at least 300 genes. Subsequently, the Seurat objects were merged to create a single Seurat object. Cells with RNA counts between 300 and 4000 and a mitochondrial gene percentage of less than 9% were selected for downstream analysis. Gene expression values were log-normalized with the default parameters and scaled for the top 3000 variable genes. The scaled data was then used to compute the 50 principal components. Cells were iteratively clustered using the Louvain algorithm after identifying neighboring cells. Differentially expressed genes for each cluster were identified using genes that are detected in at least 10% of cells in either of the two clusters and genes showing a minimum difference of 10% between the two clusters. Cell types were annotated using known marker genes. Finally, the data was visualized using UMAP.
SABER-seq barcode analysis was performed using the following protocol. The SABER-seq FASTQ reads were processed using the Cell Ranger count pipeline.A bash script was then used to generate a text file containing all FASTQ headers and error-corrected cell barcodes for SABER-seq data. Error-corrected cell barcodes from transcriptomic reads were isolated and matched against those in the text file to identify common cell barcode that are shared between the transcriptomic and SABER-seq datasets. The resulting text file contained redundant error corrected cell barcodes associated with different UMIs for the same cell. Thus, unique error corrected cell barcodes were isolated to create a text file containing unique FASTQ headers and error-corrected barcodes. Subsequently, FASTQ reads matching the FASTQ headers in this file were extracted from the SABER-seq raw reads using a Python script. SABER-seq barcodes were analyzed using the scGESTALT pipeline available on Github as described previously. To analyze differences in barcode detection and editing frequencies between cell types a binomial test was used.
genome build/assembly: GRCz11
processed data files format and content: *.h5 files contain filtered features/genes and barcode data generated from cell ranger pipeline.
processed data files format and content: LinC1_Filtered_Fastq_Headers_CB.txt,LinC2_Filtered_Fastq_Headers_CB.txt,LinD1_Filtered_Fastq_Headers_CB.txt,LinD2_Filtered_Fastq_Headers_CB.txt,LinD3_Filtered_Fastq_Headers_CB.txt files contain filtered and unique fastq headers and cell barcodes after matching the trasncriptomic cell barcodes.
processed data files format and content: SABERb1_linC1_S4_BrainC1_S6.CB.xlsx,SABERb1_linC2_S5_BrainC2_S7.CB.xlsx,SABERb2_linD1_S1_BrainD1_S8.CB.xlsx,SABERb2_linD2_S2_BrainD2_S9.CB.xlsx,SABERb2_linD3_S3_BrainD3_S10.CB.xlsx,SABERb4_linB2.1-13.123.2.With.Primer.stats.xlsx,SABERb4_linB2.2-14.124.2.With.Primer.stats.xlsx files contain the SABER-Seq output after matching reads to the reference sequence.

extract_protocol:
Wild type and SABER x her4.3:switchCas9 zebrafish brains were harvested and dissociated at 21-23 dpf as described previously (Raj et. al 2018, Nature Biotechnology)  with the following modifications. All microcentrifuge tubes were treated with 1% BSA/DPBS overnight to prevent cell loss due to adhesion. Brains were dissociated with 1 mL of 20 units/ml papain in EBSS media and incubated at 37 °C for 20 min. Cells were resuspended with ~150 μl ice cold 1%BSA/DPBS solution.
Transcriptome libraries were processed according to the manufacturer’s instructions (Single Cell 3’ v3 kit). Transcriptome libraries were sequenced using NovaSeq S4 300 cycle kits (Novogene) and Novaseq SP 100 and 200 cycle kits (MedGenome). To generate SABER-seq libraries, samples post cDNA amplification and prior to fragmentation were split into two parts. One part was processed for transcriptome libraries as instructed by the manufacturer. The other part was processed for SABER-seq libraries as follows. To enrich for SABER barcodes, 5 µl of the whole transcriptome cDNA was PCR amplified with 10X_p140v1UP  (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT CGTCGTAGATCTTCATCGTGATG) and 10XPCR1F (CTACACGACGCTCTTCCGATCT) primers and Q5 polymerase. The reaction conditions were: 98 °C, 30 s; [98 °C, 10 s; 68 °C, 25 s; 72 °C, 15 s] x 14 cycles; 72 °C, 2 min. The reaction was cleaned up with 0.8X SPRISelect beads and eluted in 20 µl elution buffer (EB) buffer. A second PCR was carried out using 3 µl of PCR1 product and 10XPCR1F and 10X_p140v2Sa (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT GAAACTACATGGGGTcaGCTC) primers. Reaction conditions were same as PCR1 except only 13 cycles were completed. At this point, 2 different clean up conditions were used: iteration 1 (SABER-seq_v0) and iteration 2 (SABER-seq_v1). For iteration 1, the reaction was cleaned up with 0.8X SPRISelect beads and eluted in 20 µl elution buffer (EB) buffer similar to PCR1.  For iteration 2, an optimization was trialed, and the reaction was cleaned up with right side size selection using SPRIselect beads (0.6X beads used initially and supernatant was rebound with 1.5X beads). The product was eluted in 20 µl EB. Finally, adapters and sample indices were incorporated in a third PCR reaction using 5-7 µl of a 1:10 dilution of PCR2 product. Reactions conditions were same as PCR1 except 9-10 cycles were completed. Primers used: 10XP5Dual_Hx (AATGATACGGCGACCACCGAGATCTACAC-xxxxxxx xxx-ACACTCTTTCCCTACACGACGCTCTTCCGATCT), 10XP7Dual_H5 (AATGATACGGCGAC CACCGAGATCTACAC-xxxxxxxxxx-ACACTCTTTCCCTACACGACGCTCTTCCGATCT), where x represents index bases from the 10X Dual Index Kit TT, SetA H index entries. For iteration 1, the third PCR reaction was cleaned up with 0.8X SPRISelect beads and eluted in 20 µl elution buffer (EB) to generate final libraries. For iteration 2, the third PCR reaction was cleaned up with right side size selection using SPRIselect beads (0.65X beads used initially and supernatant was rebound with 1.5X beads). SABER-seq libraries were sequenced using Novaseq SP 200 cycle kits (MedGenome) with 5-10% PhiX spike-in. Sequencing parameters: Read1 28 cycles, Read2 151 cycles, Index1 10 cycles, Index2 10 cycles. Standard sequencing primers were used.


title: MC_D6_TGF_2

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

description:
MC_D6_TGF_2
processed_dev.rds

data_processing:
Reads were pseudoaligned to the GrCH38 assembly using Kallisto (Bray et al, 2016) with default settings.
Gene-level expression data was imported into R using TXImport (Soneson et al, 2015)
Assembly: GrCH38
Supplementary files format and content: TXImport file containing abundance, counts, and length

source_name: Peripheral blood

growth_protocol: Buffy coats from de-identified donors purchased from Research Blood Components, LLC. Pperipheral blod mononuclear clels were isolated using Ficoll paque density gradient centrifugation, and CD34+ cells isolated using magnetic beads. Isolated cells were seeded at 150,000 cells/ml in StemSpan SFEM media supplemented with SCF (100ng/ml), IL-6 (50 ng/ml) and penicillin/streptomycin (1:100 dilution), with IL-3 (1 ng/ml) added for the first three weeks of culture. For PB-MCT differentiation, TGF-b1 (1 ng/mL) was added for the full culture duration.

extract_protocol:
Cells were spun down and resuspended in TCL buffer (Qiagen) with 1% 2-mercaptoethanol. Lysate containing 1,000 cells was transferred into low-bind plates for sequencing through the Broad Institute Genomics Platform
SmartSeq2 libraries were prepared according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads. Poly(A)+ mRNA was converted to cDNA which was then amplified. cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out using an Illumina NextSeq500 as paired- end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: For 24h and 6d groups, differentiated MCs were cultured in StemSpan SFEM media supplemented with 100 ng/ml SCF in the presence or absence of TGF-b1 (1 ng/ml) for the indicated time period.

value: Peripheral blood

value: Mast cell

value: Differentiated for seven weeks in SCF,  IL-6, and TGF-b1, supplemented with IL-3 for the first three weeks


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day6 rep 3

city: New York

first: Arturo

last: Marin Alguacil

address: One Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
counts_Day2_mock_vs_Day6_rWT.txt
edger_Day2_mock_vs_Day6_rWT.csv
deseq2_Day2_mock_vs_Day6_rWT.csv

data_processing:
The reads from the illumina paired-end sequencing were processed with the Trimmomatic v0.36 program to filter out low-quality reads and to trimme the adapters (parameters- ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:30).
Filtered and trimmed reads were mapped against Mesocricetus auratus genome (GCF_017639785.1) using HISAT2 v2.2.1 .
The featureCounts v2.0.1 software was used for the counting process.
Assembly: BCM_Maur_2.0
Supplementary files format and content: Tab-delimited .txt files containing the counts. These files contain a header with the executed command.
Supplementary files format and content: Comma-separated values files (.csv) with the normaliced counts with edgeR or DESeq2 software.

molecule: polyA RNA

organism: Mesocricetus auratus

source_name: lung

extract_protocol:
Samples for RNA sequencing were lysed in Trizol Reagent and total RNA was extracted using the miRNeasy mini kit (Qiagen) per the manufacturer’s instructions. DNAse treatment was performed on isolated RNA using the RNA Clean and Concentrator Kit (Zymo).
illumina Stranded mRNA. RNA polyA selection.

value: lung

tag: infection

value: SARS-CoV-2 WA1 (Wild Type virus)

tag: time


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day6 rep 4

tag: tissue


title: SABERb4_brainB2_1, brain4, transcriptome

description:
SABERb4.1_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds

value: zebrafish whole brain

value: 21-23 dpf, Juvenile


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day6 rep 2


title: SABERb3_brainB1_2, brain3, transcriptome

description:
SABERb3.2_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds

value: WT/TLAB


title: MC_D6_TGF_1

description:
MC_D6_TGF_1
processed_dev.rds


title: MC_D5_TGF_2

description:
MC_D5_TGF_2
processed_dev.rds


title: media_sham_6h_exp1_1

value: No injury (Sham)

value: 6 Hours Post-Injury


title: media_CCI_6h_exp2_6

value: Controlled Cortical Impact (CCI)

value: miRNA


title: SABERb1_linC2, brain1, SABER-Seq

description: 10X Genomics


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day6 rep 1


title: SABERb3_brainB1_1, brain3, transcriptome

description:
SABERb3.1_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds


title: media_CCI_6h_exp2_5


title: MC_D5_TGF_1

description:
MC_D5_TGF_1
processed_dev.rds


title: SABERb2_brainD3091523wk3, Novogene_Run1, brain2, transcriptome

description:
SABERb2_transcriptomic_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day4 rep 4

description:
counts_Day2_mock_vs_Day4_rWT.txt
edger_Day2_mock_vs_Day4_rWT.csv
deseq2_Day2_mock_vs_Day4_rWT.csv


title: MC_D4_TGF_2

description:
MC_D4_TGF_2
processed_dev.rds


title: SABERb2_brainD2091523wk3, Novogene_Run1, brain2, transcriptome


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day4 rep 3


title: media_sham_24h_exp2_4

value: 24 Hours Post-Injury


title: media_CCI_6h_exp2_3


title: media_CCI_6h_exp2_4


title: MC_D4_TGF_1

description:
MC_D4_TGF_1
processed_dev.rds

value: Differentiated for seven weeks in SCF,  IL-6, and TGF-b1, supplemented with IL-3 for the first two weeks


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day4 rep 2


title: SABERb2_brainD1091523wk3, Novogene_Run1, brain2, transcriptome


title: media_CCI_6h_exp2_2


title: MC_D6_ctrl_2

description:
MC_D6_ctrl_2
processed_dev.rds

value: Differentiated for seven weeks in SCF and IL-6, supplemented with IL-3 for the first three weeks


title: SABERb2_brainD3, Medgenome_Run2, brain2, transcriptome


title: MC_D6_ctrl_1

description:
MC_D6_ctrl_1
processed_dev.rds


title: media_CCI_6h_exp2_1


title: media_CCI_6h_exp1_6


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day4 rep 1


title: MC_D5_ctrl_2

description:
MC_D5_ctrl_2
processed_dev.rds


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day2 rep 4

description:
counts_Day2_mock_vs_Day2_rWT.txt
edger_Day2_mock_vs_Day2_rWT.csv
deseq2_Day2_mock_vs_Day2_rWT.csv


title: SABERb2_brainD2, Medgenome_Run2, brain2, transcriptome


title: SABERb2_brainD1, Medgenome_Run2, brain2, transcriptome


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day2 rep 3


title: media_CCI_6h_exp1_5


title: SABERb1_brainC2091523wk3, Novogene_Run1, brain1, transcriptome

description:
SABERb1_transcriptomic_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day2 rep 2


title: media_CCI_6h_exp1_4


title: MC_D4_ctrl_2

description:
MC_D4_ctrl_2
processed_dev.rds


title: MC_D5_ctrl_1

description:
MC_D5_ctrl_1
processed_dev.rds


title: SABERb1_brainC1091523wk3, Novogene_Run1, brain1, transcriptome


title: MC_D4_ctrl_1

description:
MC_D4_ctrl_1
processed_dev.rds


title: RNA-seq of Mesocricetus auratus: adult female (lung), infected day2 rep 1


title: media_CCI_6h_exp1_3


title: RNA-seq of Mesocricetus auratus: adult female (lung), not infected day2 rep 4

description:
counts_Day2_mock_vs_Day2_rWT.txt
edger_Day2_mock_vs_Day2_rWT.csv
deseq2_Day2_mock_vs_Day2_rWT.csv
counts_Day2_mock_vs_Day4_rWT.txt
edger_Day2_mock_vs_Day4_rWT.csv
deseq2_Day2_mock_vs_Day4_rWT.csv
counts_Day2_mock_vs_Day6_rWT.txt
edger_Day2_mock_vs_Day6_rWT.csv
deseq2_Day2_mock_vs_Day6_rWT.csv

value: not infected (mock)


title: MC_D3_TGF_6d_2

description:
MC_D3_TGF_6d_2
processed_6d.rds

value: 100 ng/ml SCF plus 1 ng/mL TGF-b1 for 6 days


title: media_CCI_6h_exp1_2


title: SABERb1_brainC2, Medgenome_Run2, brain1, transcriptome


title: RNA-seq of Mesocricetus auratus: adult female (lung), not infected day2 rep 3


title: MC_D3_TGF_6d_1

description:
MC_D3_TGF_6d_1
processed_6d.rds

value: Peripheral blood


title: SABERb1_brainC1, Medgenome_Run2, brain1, transcriptome


title: media_CCI_6h_exp1_1


title: zBrHb_C1hind021023wk3, hindbrain, transcriptome

description:
hb_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds

source_name: zebrafish hindbrain

value: zebrafish hindbrain


title: SNU216 cells, siOXTR_3

city: Shenyang

first: Xin

last: Li

state: China/Liaoning province

address: Puhe road

institute: China Medical University

description: Library name: Sample 6

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
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.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: text files include RPKM values for each sample

source_name: gastric cancer

growth_protocol: SNU216 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Lysis of cells with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using BGISEQ-500 protocols.

treatment_protocol: SNU216 cells were transfected with siControl and siOXTR for 48 h.

value: gastric cancer


title: SNU216 cells, siOXTR_2

description: Library name: Sample 5


title: RNA-seq of Mesocricetus auratus: adult female (lung), not infected day2 rep 2

value: lung


title: MC_D2_TGF_6d_1

description:
MC_D2_TGF_6d_1
processed_6d.rds

value: Mast cell


title: zBrMb_B1mid021023wk3, midbrain, transcriptome

description:
mb_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds

source_name: zebrafish midbrain

value: zebrafish midbrain


title: MC_D2_TGF_6d_2

description:
MC_D2_TGF_6d_2
processed_6d.rds


title: SNU216 cells, siOXTR_1

description: Library name: Sample 4


title: pair2, inter, 100% CICI, rep2

city: State College

first: Yi

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

description: Library name: pair2_100_rep2

data_processing:
Next generation sequencing was performed on NextSeq 2000, and 100 million of  50 bp paired-end reads were generated for each replicate. Hi-C data analysis was performed with HiC-pro (version 3.1.0), cooler(version 0.10.0), cooltools (version 0.7.0) and HiCExplorer (version 3.7.2).
Assembly: sacCer3
Supplementary files format and content: cool files

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in 200 mL SCD-Met medium until OD660 reached 0.3.

extract_protocol:
Standard method was used to perform Hi-C and extract DNA.
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: To arrest cells in the G1 phase, 80 µM alpha-factor (Zymo, Y1001) was added to the culture for a total of 2.5 hours. During the final hour of this incubation, 1 ng/µL rapamycin was added to induce CICI. DMSO was added in the control group instead. After 1 hour of rapamycin treatment, cells were harvested for imaging analysis and Hi-C measurement.

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::966175_LacO, Chr4::1166682_TetO

value: 100% CICI cell + 0% DMSO cell


title: zBrFb_A1fore021023wk3, forebrain, transcriptome

description:
fb_filtered_feature_bc_matrix.h5
upd.wk3.res.1.0.rds
upd1.neu.3.0.rds
Neur.Diff.res.0.3.rds
Di.res.0.2.rds
GC.res.0.45.rds
Tel.res.0.4.rds
Pa.res.0.3.rds
Pallium.res.0.5.rds
SubPal.res.0.4.rds
OT.res.0.2.rds
opt.sub.res.0.5.rds
DHab.res.0.2.rds
VHab.res.0.7.rds
Hyp.res.0.2.rds
Prog.res.0.13.rds
RGC.URL.res.0.2.rds
PurN.rds
MB.res.0.1.rds
HB.res.0.2.rds

source_name: zebrafish forebrain

value: zebrafish forebrain

value: 21-23 dpf, Juvenile

value: WT/TLAB


title: SNU216 cells, siControl_3

description: Library name: Sample 3


title: pair2, inter, 50% CICI, rep2

description: Library name: pair2_50_rep2

value: 50% CICI cell + 50% DMSO cell


title: SNU216 cells, siControl_1

description: Library name: Sample 1


title: MC_D1_TGF_6d_1

description:
MC_D1_TGF_6d_1
processed_6d.rds


title: SNU216 cells, siControl_2

description: Library name: Sample 2


title: pair2, inter, 20% CICI, rep2

description: Library name: pair2_20_rep2

value: 20% CICI cell + 80% DMSO cell


title: MC_D1_TGF_6d_2

description:
MC_D1_TGF_6d_2
processed_6d.rds


title: MmuPV1

city: Charleston

first: Heehwa

last: Son

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

hyb_protocol: Custom probe hybridization, ligation, amplification, cell segmentation staining, and autofluorescence quenching was performed according to manufacturer protocols “Xenium In Situ Gene Expression with Cell Segmentation Staining - User Guide CG000749 Rev A.”

scan_protocol: Xenium In Situ Analyzer

data_processing: The Xenium Onboard Analysis platform was used to generate cell segmentaion, gene transcript-by-cell, and transcript-by-tissue location data matrics.

source_name: Skin

label_protocol: Xenium mouse probe set

extract_protocol: FFPE mouse back skin sapmes, infected with MmuPV1 (n =2, pooled onto one slide) versus VLP (n =2, pooled onto one slide) followed by UV skin treatment, were sliced onto Xenium capture areas according to “Xenium In Situ for FFPE - Tissue Preparation Guide CG000578 Rev C” before delivering slides to the Spatial Technology Platform

treatment_protocol: The back skin of SKH-1 were colonized with MmuPV1 or virus-like particle VLP. Following virus colonization, mice received 50 µg DMBA in 200 μL acetone on the back skin (Week 0). After one week, mice were exposed to 150 mJ/cm2 ultraviolet B (UV) 3 times per week for up to 25 weeks.

tag: gender

value: female


title: VLP


title: lin-35 glp-4 rep 2

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
Library name: lin-35_glp-4_rep2
16-30 nt purified RNAs from co-IPs

data_processing:
Small RNA data processing was done using the default configuration in the tinyRNA pipeline (https://github.com/MontgomeryLab/tinyRNA)
Assembly: WS279
Supplementary files format and content: glp-4-wt_norm_counts.csv
Supplementary files format and content: glp-4-bn2-mut_norm_counts.csv

organism: Caenorhabditis elegans

source_name: sterile hermaphroditic adult whole animals grown at 25C

growth_protocol: Eggs were hatched and arrested as synchronous L1 larvae and then plated on E. coli OP50 and grown at either 20 ̊C (glp-4+) for 78-96 hours or 25 ̊C (glp-4-) for 72-74 hours, at which time most animals had reached adult stage.

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. RNA was isolated using trizol/chloroform and isopropanol precipitation.
Total RNA was treated with NEB RNA 5' Pyrophosphohydrolase (RppH) to facilitate capture of 22G-RNAs. ~16-30-nt small RNAs were purified from total RNA by size selection using 17% polyacrylamide gels. Libraries were then prepared according to the NEBNext Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected on 10% polyacrylamide gels.

tag: genotype


title: MC_D3_PBS_6d_1

description:
MC_D3_PBS_6d_1
processed_6d.rds

value: 100 ng/ml SCF for 6 days


title: Decidua, DT+Treg treated  5

city: Adelaide

first: Ha

middle: Manh

last: Tran

state: SA

address: 4 North Terrace

country: Australia

institute: University of Adelaide

data_processing:
Sequencing libraries were prepared from high-integrity RNA (RIN>7) using the Illumina TruSeq stranded protocol and sequenced on the Illumina NovaSeq X platform at a depth of ~80 million reads per sample. Sequence read quality was accessed by FastQC (v0.12.1, ref), trimmed with cutadapt (v.1.18, ref) and aligned to GRCm38 (mm10) mouse genome and reads quantified using STAR (v2.7.10b_alpha_230301, ref).
Assembly: GRCm38 (mm10)
Supplementary files format and content: comma-separated values (csv) of raw counts

source_name: Decidual tissue

extract_protocol:
Decidual tissues were homogenized and RNA extracted as described previously (12). Successful DNA removal was confirmed and RNA concentration was measured using a Nano-drop Spectrophotometer ND- 1000 (Thermo Fisher Scientific), and RNA integrity was assessed by RNA Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) to ensure all RNA samples had an RNA integrity number of >7. To measure mRNA expression, total DNase-treated RNA was reversed transcribed into cDNA from 800 ng RNA primed with 50 ng random hexamers using SuperscriptIV Reverse Transcription kit (Life Technologies) according to the manufacturer’s instruction. qPCR was performed using 20 ng cDNA and PCR primers
Stranded polyA libraries prepared using Nugen Universal Plus mRNA-seq (Part No. 0508), protocol M01442 v2.

value: Decidual tissue

value: d10.5 post coitum

tag: Sex

value: DT treated + adoptive transfer of WT Treg


title: lin-35 glp-4 rep 1

description:
Library name: lin-35_glp-4_rep1
16-30 nt purified RNAs from co-IPs

value: sterile hermaphroditic adult whole animals grown at 25C


title: Decidua, DT+Treg treated  4


title: pair2, inter, 0% CICI, rep2

description: Library name: pair2_0_rep2

value: 0% CICI  cell + 100% DMSO cell


title: lin-15b glp-4 rep 2

description:
Library name: lin-15b_glp-4_rep2
16-30 nt purified RNAs from cell lysate


title: pair2, inter, 10% CICI, rep2

description: Library name: pair2_10_rep2

value: 10% CICI  cell + 90% DMSO cell


title: Decidua, DT+Treg treated  3


title: RNA-seq of Mesocricetus auratus: adult female (lung), not infected day2 rep 1

value: lung

value: not infected (mock)


title: MC_D2_PBS_6d_2

description:
MC_D2_PBS_6d_2
processed_6d.rds

value: Peripheral blood

value: Mast cell


title: pair1, intra, 100% CICI, rep2

description: Library name: pair1_100_rep2

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::793958_TetO

value: 100% CICI cell + 0% DMSO cell


title: MC_D2_PBS_6d_1

description:
MC_D2_PBS_6d_1
processed_6d.rds


title: lin-15b glp-4 rep 1

description:
Library name: lin-15b_glp-4_rep1
16-30 nt purified RNAs from cell lysate


title: pair1, intra, 50% CICI, rep2

description: Library name: pair1_50_rep2


title: MC_D1_PBS_6d_2

description:
MC_D1_PBS_6d_2
processed_6d.rds


title: Decidua, DT+Treg treated  2


title: glp-4 rep 2

description:
Library name: glp-4_rep2
16-30 nt purified RNAs from cell lysate


title: Decidua, DT+Treg treated  1


title: MC_D3_PBS_6d_2

description:
MC_D3_PBS_6d_2
processed_6d.rds


title: MC_D1_PBS_6d_1

description:
MC_D1_PBS_6d_1
processed_6d.rds


title: pair1, intra, 20% CICI, rep2

description: Library name: pair1_20_rep2


title: glp-4 rep 1

description:
Library name: glp-4_rep1
16-30 nt purified RNAs from co-IPs


title: Decidua, DT treated 6

value: Diptheria toxin (DT) treated (Treg depleted)


title: pair1, intra, 10% CICI, rep2

description: Library name: pair1_10_rep2


title: MC_D3_TGF_24h_2

description:
MC_D3_TGF_24h_2
processed_24h.rds

value: 100 ng/ml SCF plus 1 ng/mL TGF-b1 for 24 hours


title: Decidua, DT treated 4


title: lin-9 rep 2

description:
Library name: lin-9_rep2
16-30 nt purified RNAs from co-IPs

source_name: gravid hermaphroditic adult whole animals grwon at 20C


title: MC_D3_TGF_24h_1

description:
MC_D3_TGF_24h_1
processed_24h.rds


title: pair1, intra, 0% CICI, rep2

description: Library name: pair1_0_rep2


title: lin-9 rep 1

description:
Library name: lin-9_rep1
16-30 nt purified RNAs from co-IPs

value: gravid hermaphroditic adult whole animals grwon at 20C


title: pair2, inter, 100% CICI, rep1

description: Library name: pair2_100_rep1

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::966175_LacO, Chr4::1166682_TetO


title: MC_D2_TGF_24h_2

description:
MC_D2_TGF_24h_2
processed_24h.rds


title: lin-52 rep 2

description:
Library name: lin-52_rep2
16-30 nt purified RNAs from co-IPs


title: Decidua, DT treated 2

value: female


title: pair2, inter, 50% CICI, rep1

description: Library name: pair2_50_rep1

value: 50% CICI cell + 50% DMSO cell


title: lin-52 rep 1

description:
Library name: lin-52_rep1
16-30 nt purified RNAs from co-IPs


title: pair2, inter, 20% CICI, rep1

description: Library name: pair2_20_rep1

value: 20% CICI cell + 80% DMSO cell


title: Decidua, DT treated 1

value: Decidual tissue

value: d10.5 post coitum


title: MC_D1_TGF_24h_2

description:
MC_D1_TGF_24h_2
processed_24h.rds


title: lin-35 rep 2

description:
Library name: lin-35_rep2
16-30 nt purified RNAs from co-IPs


title: MC_D1_TGF_24h_1

description:
MC_D1_TGF_24h_1
processed_24h.rds


title: pair2, inter, 10% CICI, rep1

description: Library name: pair2_10_rep1


title: Decidua, vehicle treated 6

value: Vehicle (PBS)


title: pair2, inter, 0% CICI, rep1

description: Library name: pair2_0_rep1

value: 0% CICI  cell + 100% DMSO cell


title: lin-35 rep 1

description:
Library name: lin-35_rep1
16-30 nt purified RNAs from cell lysate


title: Decidua, vehicle treated 4


title: pair1, intra, 100% CICI, rep1

description: Library name: pair1_100_rep1


title: lin-15b rep 2

description:
Library name: lin-15b_rep2
16-30 nt purified RNAs from cell lysate


title: MC_D3_PBS_24h_2

description:
MC_D3_PBS_24h_2
processed_24h.rds

value: 100 ng/ml SCF for 24 hours


title: Decidua, vehicle treated 3


title: lin-15b rep 1

description:
Library name: lin-15b_rep1
16-30 nt purified RNAs from cell lysate


title: MC_D3_PBS_24h_1

description:
MC_D3_PBS_24h_1
processed_24h.rds


title: N2 rep 2

description:
Library name: N2_rep2
16-30 nt purified RNAs from cell lysate

value: wild type (N2)


title: Decidua, DT treated 3


title: MC_D2_PBS_24h_2

description:
MC_D2_PBS_24h_2
processed_24h.rds

value: Peripheral blood


title: MC_D2_TGF_24h_1

description:
MC_D2_TGF_24h_1
processed_24h.rds

value: Mast cell


title: N2 rep 1

description:
Library name: N2_rep1
16-30 nt purified RNAs from cell lysate


title: Decidua, vehicle treated 2


title: Decidua, vehicle treated 1


title: pair1, intra, 10% CICI, rep1

description: Library name: pair1_10_rep1

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::793958_TetO

value: 10% CICI  cell + 90% DMSO cell


title: pair1, intra, 20% CICI, rep1

description: Library name: pair1_20_rep1


title: MC_D2_PBS_24h_1

description:
MC_D2_PBS_24h_1
processed_24h.rds


title: pair1, intra, 0% CICI, rep1

description: Library name: pair1_0_rep1


title: Parse, BCG-treated mice, replicate 2, scRNA-seq

city: Singapore

first: Mugdha

last: Patwardhan

address: 10 Medical Drive,  MD11-B1-0

country: Singapore

institute: National University of Singapore

description: Parse Biosciences

data_processing:
Reads were aligned to the mouse genome (GRCm39) with the split-pipe (v0.9.6p) program from Parse Biosciences with the release 107 Ensembl GTF annotations.
Both sublibraries were generated separately with the --mode all command and demultiplexed into 7 samples.
The filtered gene expression matrices across all samples, across both sublibraries, were then combined into a single Seurat (v4.3.0) object for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: RDS format

source_name: bladder

growth_protocol: MB49-PSA cells were cultured in high-glucose DMEM (supplemented with 1% Pen-strep, 1% L-Glutamine and 10% fetal bovine serum). MB49-PSA cells were implanted orthotopically in WT and KO female mice

extract_protocol:
Whole bladders were harvested and single cells were isolated by mechanical dissassociation of the bladder followed by collagenase treatment.
Library construction was performed according to the manufacturer's instructions (Evercode Whole Transcriptome (WT) Mini , Parse Biosciences). In brief, cells were fixed and permeabilised. Multiple rounds of split-pool-ligation were carried out for combinatorial barcoding. Pooled cells were distributed across sublibraries and then lysed, followed by reverse transcription and PCR amplification.

treatment_protocol: Mice were treated with weekly intravesical BCG instillations for 4 weeks

value: bladder

value: 4-6 months

value: 4 BCG instillations


title: Parse, BCG-treated mice, replicate 1, scRNA-seq

description: Parse Biosciences


title: MC_D1_PBS_24h_2

description:
MC_D1_PBS_24h_2
processed_24h.rds


title: MC_D1_PBS_24h_1

description:
MC_D1_PBS_24h_1
processed_24h.rds


title: Decidua, vehicle treated 5


title: atg8_nonuple_crispr_plant1

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: Library name: atg8_crispr_plant1

data_processing:
Raw FASTQ files obtained from sequencing were quality-checked and adapter-trimmed using TrimGalore (https://github.com/FelixKrueger/TrimGalore) with default settings.
The trimmed FASTQ files were aligned to the TAIR10 genome using Bowtie2 (Langmead & Salzberg, 2012) with the parameters -D 15 -R 2 -N 0 -L 22 -i S,1,1.15.
The resulting aligned BAM files were sorted and indexed using SAMtools (Danecek et al., 2021) .
Deletionsa nd insertions were manually inspected using the Integrative Genomics Viewer (IGV).
Assembly: TAIR10

source_name: 10 days old seedling

extract_protocol:
DNA was extracted using the cetyltrimethylammonium bromide (CTAB)
Illumina-compatible libraries with the Nextera XT DNA Library Preparation Kit, following the manufacturer’s instructions.

value: 10 days old seedling


title: atg8_nonuple_crispr_plant2

description: Library name: atg8_crispr_plant2


title: pair1, intra, 50% CICI, rep1

description: Library name: pair1_50_rep1


title: blood_NLCB_00309

status: Public on Dec 10 2024

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

description:
401_00309
Specimen 00309 from the NLCB biobank, sampled on PAXgene tubes

hyb_protocol: Biotin-labelled cRNA was hybridized to Illumina HumanHT-12 v4 Expression BeadChips (Illumina, Inc., San Diego, CA, USA) according to the manufacturer's protocol.

scan_protocol: Microarrays were scanned with the BeadArray Reader (Illumina).

data_processing:
Illumina BeadArray studio (Illumina) was used to handle Illumina data. Data analysis was performed using R (http://cran.r-project.org), together with tools from the Bioconductor project (lumi package). The recommended detection score cut off suggested by the lumi detectionCall function was used, leaving data from 30,715 of 47,323 probes to be used for further analyses. The 30,715 probes were log2-transformed and normalized using quantile–quantile normalization.  We corrected for differences in gene expression between the PAXgene and Tempus systems by using a separate set of control samples to measure latent expression differences between PAXgene and Tempus for each gene (ArrayExpress accession number: E-MTAB-5138; PMID: 28335817; doi: 10.1186/s13104-017-2455-6). These gene-specific expression differences were then subtracted from the gene expression values in samples isolated from PAXgene tubes.
R and the Bioconductor package lumi was used to normalize the data as follows:  Assume that the non-normalized expression data filtered for detected probes is stored as a LumiBatch object in the variable data, that the probe-specific logFC expression differences between PAXgene and Tempus are stored as a vector in the variable delta, and that the indexes of samples that should be batch corrected (i.e. PAXgene samples) are stored in the variable pax. The following steps in R would then normalize the data:
data.t <- lumiT(data, method=log2)
data.q <- lumiN(data.t, method=quantile)
data.n <- data.q
e.data <- exprs(data.n)
e.data[,pax] <- e.data[,pax] - delta
exprs(data.n) <- e.data
Matrix_non-normalized.txt includes the raw unfiltered and unnormalised data, as output from Illumina's GenomeStudio version 1.9.0.

source_name: peripheral whole blood

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA) was used to amplify RNA for hybridization on Illumina BeadChips. Total RNA was used in the first strand cDNA synthesis by reverse transcription. Following the second strand cDNA synthesis and cDNA purification steps, in vitro transcription to synthesize cRNA was carried out for 12 h.

extract_protocol: Total content in the tubes (blood and preservative in either PAXgene or Tempus) was diluted with 1× PBS (1:1 vol of blood: 1× PBS). The tubes were subsequently vortexed for 30 s before centrifugation for 60 min (4500 rcf, 4 °C) using a swing out rotor. The supernatant was removed and the tubes were decanted upside down for 2 min to dry. Buffer 1 (350 μL) from the PAXgene kit was added and the pellet was dissolved by pipetting up and down. The samples were transferred to sterile 1.5 mL tubes (Eppendorf AG, Hamburg, Germany) before adding Buffer 2 (300 μL) and proteinase K (40 μL), both from the PAXgene kit. The samples were vortexed and incubated for 10 min at 55 °C using a shaker incubator (1200 rpm, Eppendorf thermomixer comfort, Eppendorf). After a quick spin down, the lysate was directly pipetted to a PAXgene spin column and centrifuged for 3 min (1500 rcf). The supernatant was transferred to a new tube and 100% ethanol (812 μL, 1.25 times the present volume) was added and mixed by turning the tube upside down. The lysate- and ethanol mix was transferred to filter from the mirVana kit (Life Technologies, Part Number AM1560), centrifuged for 15 s (9000 rcf) and the flow-through was discarded. Since the filter has a maximum volume of 700 μL, this process was repeated until all the mix was run through. Wash solution 1 (700 μL) from the mirVana kit (Life Technologies) was added and the samples were centrifuged for 15 s (9000 rcf). The flow-through was subsequently discarded before 500 μL Wash solution 2/3 (Life Technologies) was added. The samples were again centrifuged for 15 s (9000 rcf). The flow-through was discarded before treating with DNase1 (80 µL) (PreAnalytiX) for 15 min at room temperature. The filter was washed with a second round of Wash solution 2/3 (500 μL), and centrifuged for 15 s (9000 rcf). The filter was dried for one min by centrifuging (9000 rcf) before it was transferred to a new collection tube. To elute the RNA 50, μL pre-heated nuclease free water (Tempus kit, Applied Biosystems) was added followed by spinning for 30 s (9000 rcf). The elution step was repeated and the tubes were centrifuged for 2 min. The eluate was transferred to a new sterile 1.5 mL tube (Eppendorf AG) without disturbing the debris. Finally, the samples were incubated at 65 °C for 5 min before RNA yield and quality were measured.

treatment_protocol: Cancer samples: During diagnostic work-up under the suspicion of presence of lung cancer, venous blood was collected by phlebotomy with butterfly needle from 123 patients with their consent. Blood was collected into PAXgene tubes. All samples were inverted 10 times before being stored at -80°C. Prior to isolation of RNA, the tubes were thawed at room temperature for 16 h as recommended by the PAXgene protocol for enhanced yields.  Control samples, NOWAC cohort: A total of 63 samples from healthy women from the Norwegian Women and Cancer Cohort (NOWAC) was drawn on PAXgene tubes with their consent.  Control samples, HUNT cohort: A total of 118 samples from healthy volunteers, men and women, included in the HUNT study in 2008 was drawn on Tempus tubes.  All samples from the control cohorts arrived at our facility frozen and were stored at -80℃. Before RNA isolation, tubes were thawed in the dark for 16 h at room temperature.

value: peripheral whole blood

tag: biobank

value: NLCB

value: Female

value: Young

value: smoker

tag: crp

tag: Stage

value: middle

tag: histology

value: AC

tag: block

tag: outlier

value: FALSE

tag: dataset

tag: status

value: case


title: blood_NLCB_00302_mPT

description:
401_00302_mPT
Specimen 00302_mPT from the NLCB biobank, sampled on PAXgene tubes

value: SCC


title: blood_NLCB_00278

description:
401_00278
Specimen 00278 from the NLCB biobank, sampled on PAXgene tubes

value: late

value: Train/Test


title: blood_NLCB_00284

description:
401_00284
Specimen 00284 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00271_mPT

description:
401_00271_mPT
Specimen 00271_mPT from the NLCB biobank, sampled on PAXgene tubes

value: Old

value: early


title: blood_NLCB_00276

description:
401_00276
Specimen 00276 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00274

description:
401_00274
Specimen 00274 from the NLCB biobank, sampled on PAXgene tubes

value: Other


title: blood_NLCB_00253_mPT

description:
401_00253_mPT
Specimen 00253_mPT from the NLCB biobank, sampled on PAXgene tubes

value: SCLC


title: blood_NLCB_00273

description:
401_00273
Specimen 00273 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00241

description:
401_00241
Specimen 00241 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00237_mPT

description:
401_00237_mPT
Specimen 00237_mPT from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00304_mPT

description:
401_00304_mPT
Specimen 00304_mPT from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00225

description:
401_00225
Specimen 00225 from the NLCB biobank, sampled on PAXgene tubes

value: Male


title: blood_NLCB_00245

description:
401_00245
Specimen 00245 from the NLCB biobank, sampled on PAXgene tubes

value: peripheral whole blood


title: blood_NLCB_00246_mPT

description:
401_00246_mPT
Specimen 00246_mPT from the NLCB biobank, sampled on PAXgene tubes

value: NLCB


title: blood_NLCB_00217

description:
401_00217
Specimen 00217 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00220

description:
401_00220
Specimen 00220 from the NLCB biobank, sampled on PAXgene tubes

value: Female


title: blood_NLCB_00269_mPT

description:
401_00269_mPT
Specimen 00269_mPT from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00264

description:
401_00264
Specimen 00264 from the NLCB biobank, sampled on PAXgene tubes

value: Young


title: blood_NLCB_00232_mPT

description:
401_00232_mPT
Specimen 00232_mPT from the NLCB biobank, sampled on PAXgene tubes

value: smoker


title: blood_NLCB_00213

description:
401_00213
Specimen 00213 from the NLCB biobank, sampled on PAXgene tubes

value: middle


title: blood_NLCB_00208

description:
401_00208
Specimen 00208 from the NLCB biobank, sampled on PAXgene tubes

value: AC


title: blood_NLCB_00221

description:
401_00221
Specimen 00221 from the NLCB biobank, sampled on PAXgene tubes

value: FALSE


title: blood_NLCB_00223

description:
401_00223
Specimen 00223 from the NLCB biobank, sampled on PAXgene tubes

value: case


title: blood_NLCB_00214

description:
401_00214
Specimen 00214 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00293

description:
401_00293
Specimen 00293 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00227

description:
401_00227
Specimen 00227 from the NLCB biobank, sampled on PAXgene tubes

value: SCC


title: blood_NLCB_00230

description:
401_00230
Specimen 00230 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00218

description:
401_00218
Specimen 00218 from the NLCB biobank, sampled on PAXgene tubes

value: late


title: blood_NLCB_00248

description:
401_00248
Specimen 00248 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00209

description:
401_00209
Specimen 00209 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00206

description:
401_00206
Specimen 00206 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00204

description:
401_00204
Specimen 00204 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00197

description:
401_00197
Specimen 00197 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00192

description:
401_00192
Specimen 00192 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00195

description:
401_00195
Specimen 00195 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00200

description:
401_00200
Specimen 00200 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00199

description:
401_00199
Specimen 00199 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00189

description:
401_00189
Specimen 00189 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00203

description:
401_00203
Specimen 00203 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00170

description:
401_00170
Specimen 00170 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00183

description:
401_00183
Specimen 00183 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00190

description:
401_00190
Specimen 00190 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00173

description:
401_00173
Specimen 00173 from the NLCB biobank, sampled on PAXgene tubes

value: TRUE


title: blood_NLCB_00174

description:
401_00174
Specimen 00174 from the NLCB biobank, sampled on PAXgene tubes

value: Old


title: blood_NLCB_00187

description:
401_00187
Specimen 00187 from the NLCB biobank, sampled on PAXgene tubes

value: Train/Test


title: blood_NLCB_00171

description:
401_00171
Specimen 00171 from the NLCB biobank, sampled on PAXgene tubes

value: early


title: blood_NLCB_00157

description:
401_00157
Specimen 00157 from the NLCB biobank, sampled on PAXgene tubes

value: Other


title: blood_NLCB_00158

description:
401_00158
Specimen 00158 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00163

description:
401_00163
Specimen 00163 from the NLCB biobank, sampled on PAXgene tubes

value: SCLC


title: blood_NLCB_00166

description:
401_00166
Specimen 00166 from the NLCB biobank, sampled on PAXgene tubes

value: peripheral whole blood

value: Male


title: blood_NLCB_00156

description:
401_00156
Specimen 00156 from the NLCB biobank, sampled on PAXgene tubes

value: NLCB


title: blood_NLCB_00147

description:
401_00147
Specimen 00147 from the NLCB biobank, sampled on PAXgene tubes

value: Female


title: blood_NLCB_00191

description:
401_00191
Specimen 00191 from the NLCB biobank, sampled on PAXgene tubes

value: smoker


title: blood_NLCB_00151

description:
401_00151
Specimen 00151 from the NLCB biobank, sampled on PAXgene tubes

value: middle


title: blood_NLCB_00149

description:
401_00149
Specimen 00149 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00146

description:
401_00146
Specimen 00146 from the NLCB biobank, sampled on PAXgene tubes

value: Young

value: AC


title: blood_NLCB_00142

description:
401_00142
Specimen 00142 from the NLCB biobank, sampled on PAXgene tubes

value: FALSE

value: case


title: blood_NLCB_00141

description:
401_00141
Specimen 00141 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00161

description:
401_00161
Specimen 00161 from the NLCB biobank, sampled on PAXgene tubes

value: never

value: late


title: blood_NLCB_00155

description:
401_00155
Specimen 00155 from the NLCB biobank, sampled on PAXgene tubes

value: Old

value: SCC


title: blood_NLCB_00160

description:
401_00160
Specimen 00160 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00139

description:
401_00139
Specimen 00139 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00137

description:
401_00137
Specimen 00137 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00134

description:
401_00134
Specimen 00134 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00136

description:
401_00136
Specimen 00136 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00119

description:
401_00119
Specimen 00119 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00111

description:
401_00111
Specimen 00111 from the NLCB biobank, sampled on PAXgene tubes

value: Train/Test


title: blood_NLCB_00103

description:
401_00103
Specimen 00103 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00076

description:
401_00076
Specimen 00076 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00112

description:
401_00112
Specimen 00112 from the NLCB biobank, sampled on PAXgene tubes

value: Other


title: blood_NLCB_00096

description:
401_00096
Specimen 00096 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00121

description:
401_00121
Specimen 00121 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00101

description:
401_00101
Specimen 00101 from the NLCB biobank, sampled on PAXgene tubes

value: SCLC


title: blood_NLCB_00130

description:
401_00130
Specimen 00130 from the NLCB biobank, sampled on PAXgene tubes

value: peripheral whole blood

value: early


title: blood_NLCB_00113

description:
401_00113
Specimen 00113 from the NLCB biobank, sampled on PAXgene tubes

value: NLCB


title: blood_NLCB_00066

description:
401_00066
Specimen 00066 from the NLCB biobank, sampled on PAXgene tubes

value: Male


title: blood_NLCB_00063

description:
401_00063
Specimen 00063 from the NLCB biobank, sampled on PAXgene tubes

value: smoker


title: blood_NLCB_00070

description:
401_00070
Specimen 00070 from the NLCB biobank, sampled on PAXgene tubes

value: middle


title: blood_NLCB_00128

description:
401_00128
Specimen 00128 from the NLCB biobank, sampled on PAXgene tubes

value: Female


title: blood_NLCB_00058

description:
401_00058
Specimen 00058 from the NLCB biobank, sampled on PAXgene tubes

value: AC


title: blood_NLCB_00082

description:
401_00082
Specimen 00082 from the NLCB biobank, sampled on PAXgene tubes

value: Young

value: FALSE


title: blood_NLCB_00107

description:
401_00107
Specimen 00107 from the NLCB biobank, sampled on PAXgene tubes

value: case


title: blood_NLCB_00071

description:
401_00071
Specimen 00071 from the NLCB biobank, sampled on PAXgene tubes

value: late


title: blood_NLCB_00067

description:
401_00067
Specimen 00067 from the NLCB biobank, sampled on PAXgene tubes

value: Old


title: blood_NLCB_00095

description:
401_00095
Specimen 00095 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00059

description:
401_00059
Specimen 00059 from the NLCB biobank, sampled on PAXgene tubes

value: SCC


title: blood_NLCB_00099

description:
401_00099
Specimen 00099 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00054

description:
401_00054
Specimen 00054 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00064

description:
401_00064
Specimen 00064 from the NLCB biobank, sampled on PAXgene tubes

value: Train/Test


title: blood_NLCB_00198

description:
401_00198
Specimen 00198 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00051

description:
401_00051
Specimen 00051 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00033

description:
401_00033
Specimen 00033 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00037

description:
401_00037
Specimen 00037 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00020

description:
401_00020
Specimen 00020 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00014

description:
401_00014
Specimen 00014 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00032

description:
401_00032
Specimen 00032 from the NLCB biobank, sampled on PAXgene tubes

value: Other


title: blood_NLCB_00017

description:
401_00017
Specimen 00017 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00007

description:
401_00007
Specimen 00007 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00047

description:
401_00047
Specimen 00047 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00009

description:
401_00009
Specimen 00009 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00039

description:
401_00039
Specimen 00039 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00028

description:
401_00028
Specimen 00028 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00018

description:
401_00018
Specimen 00018 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00043

description:
401_00043
Specimen 00043 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00012

description:
401_00012
Specimen 00012 from the NLCB biobank, sampled on PAXgene tubes

value: SCLC


title: blood_NLCB_00011

description:
401_00011
Specimen 00011 from the NLCB biobank, sampled on PAXgene tubes

value: peripheral whole blood

value: never


title: blood_NLCB_00013

description:
401_00013
Specimen 00013 from the NLCB biobank, sampled on PAXgene tubes

value: NLCB


title: blood_NLCB_00021

description:
401_00021
Specimen 00021 from the NLCB biobank, sampled on PAXgene tubes

value: Male


title: blood_NLCB_00005

description:
401_00005
Specimen 00005 from the NLCB biobank, sampled on PAXgene tubes

value: smoker


title: blood_NLCB_00035

description:
401_00035
Specimen 00035 from the NLCB biobank, sampled on PAXgene tubes

value: middle


title: blood_NLCB_00029

description:
401_00029
Specimen 00029 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00010

description:
401_00010
Specimen 00010 from the NLCB biobank, sampled on PAXgene tubes

value: early


title: blood_NLCB_00019

description:
401_00019
Specimen 00019 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00023

description:
401_00023
Specimen 00023 from the NLCB biobank, sampled on PAXgene tubes


title: blood_NLCB_00003

description:
401_00003
Specimen 00003 from the NLCB biobank, sampled on PAXgene tubes

value: Female


title: blood_NLCB_00015

description:
401_00015
Specimen 00015 from the NLCB biobank, sampled on PAXgene tubes

value: AC


title: blood_NLCB_00004

description:
401_00004
Specimen 00004 from the NLCB biobank, sampled on PAXgene tubes

value: FALSE


title: blood_NOWAC_9B

description:
NOWAC_9B
Specimen 9B from the NOWAC biobank, sampled on PAXgene tubes

value: NOWAC

value: Young

value: Train

value: control


title: blood_NLCB_00006

description:
401_00006
Specimen 00006 from the NLCB biobank, sampled on PAXgene tubes

value: Old

value: late

value: case


title: blood_NLCB_00002

description:
401_00002
Specimen 00002 from the NLCB biobank, sampled on PAXgene tubes

value: peripheral whole blood

value: SCLC


title: blood_NOWAC_7B

description:
NOWAC_7B
Specimen 7B from the NOWAC biobank, sampled on PAXgene tubes

value: never


title: blood_NLCB_00001

description:
401_00001
Specimen 00001 from the NLCB biobank, sampled on PAXgene tubes

value: NLCB

value: Male

value: SCC


title: blood_NOWAC_4B

description:
NOWAC_4B
Specimen 4B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_7A

description:
NOWAC_7A
Specimen 7A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_34B

description:
NOWAC_34B
Specimen 34B from the NOWAC biobank, sampled on PAXgene tubes

value: smoker


title: blood_NOWAC_34A

description:
NOWAC_34A
Specimen 34A from the NOWAC biobank, sampled on PAXgene tubes

value: Female


title: blood_NOWAC_32B

description:
NOWAC_32B
Specimen 32B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_33A

description:
NOWAC_33A
Specimen 33A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_3B

description:
NOWAC_3B
Specimen 3B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_4A

description:
NOWAC_4A
Specimen 4A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_31B

description:
NOWAC_31B
Specimen 31B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_5A

description:
NOWAC_5A
Specimen 5A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_32A

description:
NOWAC_32A
Specimen 32A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_30B

description:
NOWAC_30B
Specimen 30B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_3A

description:
NOWAC_3A
Specimen 3A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_33B

description:
NOWAC_33B
Specimen 33B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_5B

description:
NOWAC_5B
Specimen 5B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_28B

description:
NOWAC_28B
Specimen 28B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_9A

description:
NOWAC_9A
Specimen 9A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_2B

description:
NOWAC_2B
Specimen 2B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_31A

description:
NOWAC_31A
Specimen 31A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_29A

description:
NOWAC_29A
Specimen 29A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_2A

description:
NOWAC_2A
Specimen 2A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_30A

description:
NOWAC_30A
Specimen 30A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NLCB_00114

description:
401_00114
Specimen 00114 from the NLCB biobank, sampled on PAXgene tubes

value: early

value: Other


title: blood_NOWAC_29B

description:
NOWAC_29B
Specimen 29B from the NOWAC biobank, sampled on PAXgene tubes

value: NOWAC

value: FALSE


title: blood_NLCB_00126

description:
401_00126
Specimen 00126 from the NLCB biobank, sampled on PAXgene tubes

value: Young


title: blood_NOWAC_24A

description:
NOWAC_24A
Specimen 24A from the NOWAC biobank, sampled on PAXgene tubes

value: Train

value: control


title: blood_NOWAC_23B

description:
NOWAC_23B
Specimen 23B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_27A

description:
NOWAC_27A
Specimen 27A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_22B

description:
NOWAC_22B
Specimen 22B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_26A

description:
NOWAC_26A
Specimen 26A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_25A

description:
NOWAC_25A
Specimen 25A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_24B

description:
NOWAC_24B
Specimen 24B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_21A

description:
NOWAC_21A
Specimen 21A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_21B

description:
NOWAC_21B
Specimen 21B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_28A

description:
NOWAC_28A
Specimen 28A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_20B

description:
NOWAC_20B
Specimen 20B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_23A

description:
NOWAC_23A
Specimen 23A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_1B

description:
NOWAC_1B
Specimen 1B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_22A

description:
NOWAC_22A
Specimen 22A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_25B

description:
NOWAC_25B
Specimen 25B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_19A

description:
NOWAC_19A
Specimen 19A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_1A

description:
NOWAC_1A
Specimen 1A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_18A

description:
NOWAC_18A
Specimen 18A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_17B

description:
NOWAC_17B
Specimen 17B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_16B

description:
NOWAC_16B
Specimen 16B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_17A

description:
NOWAC_17A
Specimen 17A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_20A

description:
NOWAC_20A
Specimen 20A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_15A

description:
NOWAC_15A
Specimen 15A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_18B

description:
NOWAC_18B
Specimen 18B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_16A

description:
NOWAC_16A
Specimen 16A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_19B

description:
NOWAC_19B
Specimen 19B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_15B

description:
NOWAC_15B
Specimen 15B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_13B

description:
NOWAC_13B
Specimen 13B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_12A

description:
NOWAC_12A
Specimen 12A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_12B

description:
NOWAC_12B
Specimen 12B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_14A

description:
NOWAC_14A
Specimen 14A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_10B

description:
NOWAC_10B
Specimen 10B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_NOWAC_11A

description:
NOWAC_11A
Specimen 11A from the NOWAC biobank, sampled on PAXgene tubes

value: Old


title: blood_HUNT_93

description:
HUNT_93
Specimen 93 from the HUNT biobank, sampled on Tempus tubes

value: HUNT

value: Test


title: blood_HUNT_95

description:
HUNT_95
Specimen 95 from the HUNT biobank, sampled on Tempus tubes

value: peripheral whole blood


title: blood_HUNT_90

description:
HUNT_90
Specimen 90 from the HUNT biobank, sampled on Tempus tubes


title: blood_NOWAC_14B

description:
NOWAC_14B
Specimen 14B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_HUNT_92

description:
HUNT_92
Specimen 92 from the HUNT biobank, sampled on Tempus tubes


title: blood_NOWAC_13A

description:
NOWAC_13A
Specimen 13A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_HUNT_9

description:
HUNT_9
Specimen 9 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_86

description:
HUNT_86
Specimen 86 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_87

description:
HUNT_87
Specimen 87 from the HUNT biobank, sampled on Tempus tubes


title: blood_NOWAC_27B

description:
NOWAC_27B
Specimen 27B from the NOWAC biobank, sampled on PAXgene tubes


title: blood_HUNT_84

description:
HUNT_84
Specimen 84 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_98

description:
HUNT_98
Specimen 98 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_97

description:
HUNT_97
Specimen 97 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_89

description:
HUNT_89
Specimen 89 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_85

description:
HUNT_85
Specimen 85 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_88

description:
HUNT_88
Specimen 88 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_80

description:
HUNT_80
Specimen 80 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_83

description:
HUNT_83
Specimen 83 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_8

description:
HUNT_8
Specimen 8 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_79

description:
HUNT_79
Specimen 79 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_73

description:
HUNT_73
Specimen 73 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_75

description:
HUNT_75
Specimen 75 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_7

description:
HUNT_7
Specimen 7 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_70

description:
HUNT_70
Specimen 70 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_66

description:
HUNT_66
Specimen 66 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_67

description:
HUNT_67
Specimen 67 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_64

description:
HUNT_64
Specimen 64 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_68

description:
HUNT_68
Specimen 68 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_69

description:
HUNT_69
Specimen 69 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_63

description:
HUNT_63
Specimen 63 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_61

description:
HUNT_61
Specimen 61 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_65

description:
HUNT_65
Specimen 65 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_58

description:
HUNT_58
Specimen 58 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_71

description:
HUNT_71
Specimen 71 from the HUNT biobank, sampled on Tempus tubes


title: blood_NOWAC_26B

description:
NOWAC_26B
Specimen 26B from the NOWAC biobank, sampled on PAXgene tubes

value: never


title: blood_HUNT_60

description:
HUNT_60
Specimen 60 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_62

description:
HUNT_62
Specimen 62 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_53

description:
HUNT_53
Specimen 53 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_54

description:
HUNT_54
Specimen 54 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_57

description:
HUNT_57
Specimen 57 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_55

description:
HUNT_55
Specimen 55 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_6

description:
HUNT_6
Specimen 6 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_56

description:
HUNT_56
Specimen 56 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_52

description:
HUNT_52
Specimen 52 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_50

description:
HUNT_50
Specimen 50 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_5

description:
HUNT_5
Specimen 5 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_51

description:
HUNT_51
Specimen 51 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_47

description:
HUNT_47
Specimen 47 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_46

description:
HUNT_46
Specimen 46 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_45

description:
HUNT_45
Specimen 45 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_82

description:
HUNT_82
Specimen 82 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_35

description:
HUNT_35
Specimen 35 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_34

description:
HUNT_34
Specimen 34 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_4

description:
HUNT_4
Specimen 4 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_32

description:
HUNT_32
Specimen 32 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_39

description:
HUNT_39
Specimen 39 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_49

description:
HUNT_49
Specimen 49 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_33

description:
HUNT_33
Specimen 33 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_28

description:
HUNT_28
Specimen 28 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_29

description:
HUNT_29
Specimen 29 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_44

description:
HUNT_44
Specimen 44 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_3

description:
HUNT_3
Specimen 3 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_40

description:
HUNT_40
Specimen 40 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_27

description:
HUNT_27
Specimen 27 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_20

description:
HUNT_20
Specimen 20 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_30

description:
HUNT_30
Specimen 30 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_2

description:
HUNT_2
Specimen 2 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_26

description:
HUNT_26
Specimen 26 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_23

description:
HUNT_23
Specimen 23 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_31

description:
HUNT_31
Specimen 31 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_15

description:
HUNT_15
Specimen 15 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_19

description:
HUNT_19
Specimen 19 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_149

description:
HUNT_149
Specimen 149 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_148

description:
HUNT_148
Specimen 148 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_25

description:
HUNT_25
Specimen 25 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_144

description:
HUNT_144
Specimen 144 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_136

description:
HUNT_136
Specimen 136 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_146

description:
HUNT_146
Specimen 146 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_147

description:
HUNT_147
Specimen 147 from the HUNT biobank, sampled on Tempus tubes


title: blood_NOWAC_10A

description:
NOWAC_10A
Specimen 10A from the NOWAC biobank, sampled on PAXgene tubes


title: blood_HUNT_36

description:
HUNT_36
Specimen 36 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_141

description:
HUNT_141
Specimen 141 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_142

description:
HUNT_142
Specimen 142 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_140

description:
HUNT_140
Specimen 140 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_137

description:
HUNT_137
Specimen 137 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_135

description:
HUNT_135
Specimen 135 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_138

description:
HUNT_138
Specimen 138 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_133

description:
HUNT_133
Specimen 133 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_129

description:
HUNT_129
Specimen 129 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_130

description:
HUNT_130
Specimen 130 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_124

description:
HUNT_124
Specimen 124 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_125

description:
HUNT_125
Specimen 125 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_123

description:
HUNT_123
Specimen 123 from the HUNT biobank, sampled on Tempus tubes