title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 3MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 1MM 22 nt Rep1

status: Public on Dec 15 2025

type: SRA

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

library_source: genomic

data_processing:
The Amplicon-Seq data was analyzed using CRISPResso 2.13 (--max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap 10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 40 --min_frequency_alleles_around_cut_to_plot 0.1)
Assembly: designed sgRNA library
Supplementary files format and content: The xls file, indel frequency in each experiment.
Library strategy: Amplicon-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 cell

extract_protocol:
The gDNA was extracted using the Blood/Cells gDNA extraction kit from TIANGEN (TIANGEN DP304-03).
The target sequences were enriched from the gDNA by two rounds of PCR amplification.

tag: cell line

value: K562 cell


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 2MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 22MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 19MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 21MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 20MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 18MM 22 nt Rep1


title: SuperFi RNP electroporation at L9 site- L9 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 17MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 16MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 14MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 18MM 22 nt Rep2


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 11MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 10MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 12MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 6MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 9MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 5MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 8MM 22 nt Rep1


title: SpCas9 RNP electroporation at L5 site- L5 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 1MM 22 nt Rep1


title: SpCas9 RNP electroporation at L5 site- L5 20 nt Rep1


title: SpCas9 RNP electroporation at L9 site- L9 22 nt Rep1


title: SuperFi RNP electroporation at L5 site- L5 22 nt Rep1


title: SuperFi RNP electroporation at L5 site- L5 23 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 22MM 22 nt Rep1


title: SuperFi RNP electroporation at L5 site- L5 21 nt G Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 20MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 19MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 21MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 16MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 18MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 17MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 15MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 13MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 15MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L9 site- L9 13MM 22 nt Rep1


title: SpCas9 RNP electroporation at L9 site- L9 22 nt Rep3


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 12MM 22 nt Rep1


title: SuperFi RNP electroporation at L5 site- L5 21 nt A Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 10MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 11MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 8MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 6MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 9MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 7MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 5MM 22 nt Rep1


title: SuperFi RNP electroporation at L5 site- L5 24 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 4MM 22 nt Rep1


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 3MM 22 nt Rep1


title: SuperFi RNP electroporation at L5 site- L5 20 nt Rep1


title: SpCas9 RNP electroporation at L18 site- L18 22 nt Rep1


title: SuperFi RNP electroporation at L18 site- L18 23 nt Rep1


title: SuperFi RNP electroporation at L18 site- L18 24 nt Rep1


title: SuperFi RNP electroporation at L18 site- L18 21 nt Rep1


title: 13_ATAC

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

library_source: genomic single cell

data_processing:
Raw reads were demultiplexed and single-nucleus gene expression and peak enrichment were quantified simultaneously using CellRanger-arc count (10X Genomics). Following the quantification and peak calling analysis for each individual sample, all captures were aggregated to obtain a unified feature set for downstream analysis using CellRanger-arc aggr (10X Genomics).
All samples were analyzed together. Single cells were filtered to ensure data used in the downstream analysis is high quality: cells with >10% mitochondrial expression, indicative of dead or dying cells; cells with low numbers of genes expressed (<1000 genes) or low total UMI RNA counts (<2000 UMI counts); and cells with low peak numbers (<200 peaks) or total ATAC counts (<500 counts) were removed. Clustering was performed on the RNA-seq data, anticipating that gene expression would have a higher dynamic range than open chromatin, using the Seurat package in R. Gene expression was normalized using NormalizeData, and the top 6000 variable genes were identified using FindVariableFeatures, both with default parameters. The top variable genes were z-scored using ScaleData and principal components were computed using RunPCA for the top 200 PCs. Statistical significance of each PC was computed using JackStraw and heatmaps of the top cells and genes per PC were plotted using DimHeatmap; after reviewing both results the top 125 PCs were selected as features for clustering analysis. Clustering analysis was performed with the Louvain algorithm as implemented in Seurat at resolutions 0.25, 0.5, 1, and 2. After reviewing the expression of known marker genes, we based our downstream analysis on the clustering results at resolution 1.
In order to ensure consistency of cell annotation, we used a transfer learning approach based on scVI (10.1038/s41587-021-01206-w) and scANVI (doi.org/10.15252/msb.20209620) in which reference dataset annotations are transferred to annotate subpopulations in a new dataset. As one of our key goals was the identification and identification of immature or developing cell populations in the adult human brain, we used one human developmental forebrain scRNA-seq dataset (10.1038/s41586-018-0414-6) as well as one adult human hippocampal scRNA-seq dataset (10.1038/s41586-022-04912-w) as the reference datasets for the annotation transfer to our human adult hippocampal scRNA-seq dataset. The combination of these two datasets allowed us to train a scVI (v1.0.3) model (10.1038/s41587-021-01206-w). The latent representation was modeled using the top 5000 most variable genes in the combined dataset and was corrected for batch effect based on the data source. We then used scANVI (v1.0.3) (doi.org/10.15252/msb.20209620) (n_samples_per_label=500) to transfer the most likely label from the reference datasets to the unannotated cells in our dataset.
Assembly: hg38
Supplementary files format and content: atac_fragments.tsv.gz: gzipped tab-separated text file, fragment coordinates for all ATAC-seq alignments. Cell barcode suffixes match Sample IDs.
Supplementary files format and content: barcodes.tsv.gz: gzipped tab-separated text file, barcodes for combined multi-sample and multi-omics matrix. Cell barcode suffixes match Sample IDs.
Supplementary files format and content: features.tsv.gz: gzipped tab-separated text file, gene and peak feature list for multi-sample and multi-omics matrix.
Supplementary files format and content: matrix.mtx.gz: gzipped Matrix Market sparse matrix file, multi-sample and multi-omics matrix, covering gene expression and peak enrichment for all samples.
Supplementary files format and content: cell_metadata.txt: tab-separated text file, single-cell metadata for all cells passing QC and filtering parameters and used in final analysis, including assigned cell type, sample ID, and diagnosis.

source_name: Hippocampal tissue

extract_protocol:
The dentate gyrus was isolated from Fresh Frozen blocks of 14 participants representing 4 diagnostic groups (YA, NCI, MCI and AD). Tissue was then immediately moved to homogenization; For each sample, a separate homogenizer and douncing pestles (loose and tight) were used. Each sample was homogenized in 1ml pre-chilled lysis buffer (0.1% NP-40 Alternative (or NP-40), 10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 40U/mL of RNAse inhibitor) by mechanical douncing for 20 times with the loose pestle followed by 20 times with the tight pestle to obtain a single cell suspension. Cell suspensions were then incubated on ice for 5 minutes. The homogenate was then filtered through 70 µm filters (Milentyi Biotec 130-041-407) and 40 µm filters (Milentyi Biotec 130-041-406), moved to 1.5 ml tubes and centrifuged at 4C for 5 minutes at 500 RCF.   Supernatants were removed and the nuclei pellet was washed 3 times with wash buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2), 0.01% BSA, 40U/mL of RNAse inhibitor). After the last wash, supernatants were removed, and the nuclei pellet was resuspended in resuspension buffer and mixed with 900 µl of Sucrose Cushion buffer. To remove the additional debris, resuspended nuclei were then loaded above a 3 Sucrose Cushion gradient (2.7 ml Nuclei PURE 2M Sucrose Cushion Solution with 300 μl Nuclei PURE Sucrose Cushion Buffer) and the sucrose gradient containing the nuclei was Centrifuged at 13,000 rcf for 45 min at 4°C. The supernatant was then carefully removed and the samples were immediately processed following the Single Cell protocol from 10x Genomics.
The 10X Genomics Multiome library preparation and sequencing was done at Northwestern University NUseq facility core with the support of NIH Grant (1S10OD025120). Nuclei number was analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. The nuclei were first undergone transposition with ATAC enzyme for one hour at 37°C.  we loaded 16,000 transposed nuclei into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip J (10X Genomics, PN-1000230), and according to the manufacturer’s protocol, single cell gel beads were generated in the emulsion (GEM). Barcoded DNA and cDNA were PCR amplified and subjected to library construction. The single nuclei ATAC-seq library was generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene expression kit (10X Genomics, PN-1000281) and single Index Kit N Set A (10X Genomics, PN-1000212) according to the manufacturer’s manual. In addition, the amplified cDNA was used for the gene expression library using dual Index Kit TT Set A (10X Genomics, PN-1000215). Quality control for the constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. For the snATAC-seq library, the multiplexed libraries were pooled and sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 50 bp Read1 and 49 bp Read2. For the snRNA-seq library, the libraries were sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 28 bp Read 1 for cell barcode and UMI and 90 bp Read 2 for transcript expression. The targeted sequencing depth for snATAC-seq and snRNA-seq is 25,000 and 20,000 reads per cell, respectively.

tag: tissue

value: Hippocampal tissue

tag: diagnosis

value: YA

tag: age at_death

tag: pmi

tag: sample id

tag: library type

value: ATAC


title: SuperFi RNP electroporation at L18 site- L18 20 nt Rep1


title: SuperFi RNP electroporation at L18 site- L18 21 nt T Rep1


title: SuperFi RNP electroporation at L18 site- L18 22 nt Rep1


title: 14_ATAC


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 14MM 22 nt Rep1


title: 9_ATAC

value: MCI


title: 12_ATAC


title: 8_ATAC

value: HA


title: 10_ATAC


title: 11_ATAC


title: 7_ATAC


title: 5_ATAC


title: 4_ATAC

value: AD


title: 6_ATAC


title: 3_ATAC


title: 2_ATAC


title: 1_ATAC


title: SuperFi RNP Mismatched 22 nt gRNA electroporation at L5 site- L5 2MM 22 nt Rep1


title: 13_GEX

library_source: transcriptomic single cell

molecule: polyA RNA

value: RNA


title: 14_GEX


title: 12_GEX


title: 10_GEX


title: SpCas9 RNP electroporation at L18 site- L18 20 nt Rep1


title: 9_GEX


title: 8_GEX


title: 5_GEX


title: 3_GEX


title: 2_GEX


title: Control

city: Shanghai

first: Chuqing

last: He

address: No. 910, Hengshan Rd

department: Department of Obstetrics and Gynecology

institute: School of Medicine, Shanghai Jiaotong University

description:
scar-2
10x Genomics

library_source: transcriptomic

data_processing:
Single-cell analysis was conducted using Seurat (version 4.3.0). Potential doublets in the single-cell data were identified and removed using DoubleFinder (version 2.0) (available from https://github.com/chris-mcginnis-ucsf/DoubletFinder). Genes included in the analysis were required to be expressed in a minimum of three cells, with the total number of expressed cells that expressed >200 genes and <5000 genes. Cells with a high percentage of mitochondrial genes to total genes (> 20%) and hemoglobin genes (> 2%) were filtered out.
A total of 43,384 qualified cells were used for scRNA-seq analysis, including 18,287 qualified cells from Adjacent tissues (n = 2), 8,202 qualified cells from Control tissues (n = 1), and 16,895 qualified cells from Niche tissues (n = 2). Using Seurat, the top 2000 most variable genes were identified as highly variable genes (HVG) based on their average expression and dispersion. The dimensionality of the data was reduced using principal component analysis (PCA) on HVG. The Louvain modularity optimization algorithm was used to cluster the cells in the graph, and the clustering results were visualized using Uniform Manifold Approximation and Projection (UMAP).
Differential expression and enrichment analysis were performed to explore the cellular heterogeneity of fibroblasts and endothelial cells.
Trajectory analysis was performed to explore endothelial cells transition.
We identified a total of seven major cell types, including endometrial stroma cells (ESC, n = 6866), fibroblasts (FB, n = 8203), endothelial cells (Endo, n = 9401), epithelial cells (Epithelial, n = 1168), immune cells (Immune, n = 2993), and two types of smooth muscle cells (SMC1, n = 10,017; SMC2, n = 4736). Cell–cell communication analysis was performed to explored the interaction between fibroblasts and endothelial cells.
Assembly: hg38
Supplementary files format and content: control-1126_barcodes.tsv.gz, control-1124_barcodes.tsv.gz, CSD-1126_barcodes.tsv.gz, CSD-1224_barcodes.tsv.gz, scar-2_barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: control-1126_matrix.mtx.gz, control-1124_matrix.mtx.gz, CSD-1126_matrix.mtx.gz, CSD-1224_matrix.mtx.gz, scar-2_matrix.mtx.gz

source_name: well-healed cesarean scar

extract_protocol:
Adjacent myometrium tissue of uterine niche (Adjacent1 & Adjacent2), well-healed cesarean scar tissue (Control) and uterine niche tissue (Niche1 & Niche2) were harvested. These tissues were cut into small pieces with scissors and then incubated in DMEM medium containing collagenase I (Gibco, 17100017) and collagenase II (Gibco, 17101015) at 37°C with gentle shaking for 40-60 minutes. The digested suspension was filtered through a 100-µm cell strainer (CSS-013-100, BIOFIL). Then, the enzymatic reaction was stopped by adding 10% fetal bovine serum (FBS). The cells were pelleted by centrifugation at 350 × g for 5 minutes at 4°C. Red blood cell lysis buffer (Beyotime Biotech, C3702) was used to remove red blood cells. After removing the supernatant, the cells were resuspended in 100 μL of DMEM medium. Cell analysis was conducted using a Trypan blue cell counter, and the cell viability was consistently above 80%.
The cell concentration for loading onto the 10x Genomics Chromium™ machine ranged from 700 cells/μL to 1200 cells/μL. Cells were counted and loaded onto the Chromium Controller (10X Genomics) to recover a target of 8000 single cells. The process involved the generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction. Library quantification was performed using Qubit before pooling. The final library pool was sequenced on an Illumina Nova6000 platform using 150-base-pair paired-end reads. Aligning to the GRCh38 human genome, Cell Ranger software (version 6.0.3) was used for quality control and read counting of Ensembl genes.

value: well-healed cesarean scar


title: 4_GEX


title: 1_GEX


title: Niche2

description:
CSD-1224
10x Genomics

source_name: uterine niche

value: uterine niche


title: Adjacent 2

description:
control-1124
10x Genomics

source_name: adjacent myometrium of uterine niche

value: adjacent myometrium of uterine niche


title: Niche1

description:
CSD-1126
10x Genomics


title: Adjacent 1

description:
control-1126
10x Genomics


title: ATAC-Seq, shCHD9, rep2

city: TORONTO

first: Xin

last: Xu

state: Ontario

address: 101 COLLEGE ST EAST TOWER 11-601D

country: Canada

institute: Princess Margaret Cancer Center

data_processing:
ATAC-Seq reads were aligned to the hg38 version of the human reference genome using Bowtie2 (v2.4.5) and subsequently converted to BAM format using samtools (v1.14).
Removal of duplicate reads was accomplished using sambamba (v0.7.0). Reads originating from the mitochondria were eliminated.
Deeptools (v3.5.2) was used to generatethe bigWig files
Peak calling from bam files was performed using MACS2 (v2.2.7.1) with default parameters, ensuring a stringent threshold (q-value < 0.05).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: 22Rv1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
50,000 viable cells were resuspended in 50 uL cold ATAC-Resuspension buffer(1 M Tris-HCl, pH=7.4; 5 M NaCl; 1 M MgCl2) supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and incubate on ice for 3 minutes. The cell lysate was washed with 1 mL of cold ATAC-RSB, pelleted, and resuspended in 50 μL of transposition master mix, which consisting of 2x TD buffer (20 mM Tris-HCl, pH=7.6; 1 M MgCl2; 20% dimethyl formamide), transposase (Illumina, 20034197), PBS, 1% digitonin (Millipore, 300410), 10% Tween-20, underwent a 37°C incubation for 30 minutes with 1000 RPM mixing. The MinElute PCR purification kit (Qiagen, 28004) was employed for fragment cleanup.
Sequencing libraries were constructed using 1 x NEBnext PCR master mix and the custom primers described by Buenrostro et at (PMID: 24097267)

tag: cell type

value: human prostate cancer

tag: genotype

tag: group

value: KD CHD9


title: ATAC-Seq, shCHD9, rep1


title: ATAC-Seq, shGFP, rep2

value: shGFP

value: KD control


title: ChIP-H3K27ac, shCHD9, rep2

data_processing:
ChIP-Seq reads were aligned to the hg38 version of the human reference genome using Bowtie2 (v2.4.5) and subsequently converted to BAM format using samtools (v1.14).
Removal of duplicate reads was accomplished using sambamba (v0.7.0).
Deeptools (v3.5.2) was used to generatethe bigWig files
Peak calling from bam files was performed using MACS2 (v2.2.7.1) with default parameters, ensuring a stringent threshold (q-value < 0.05).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
ChIP assays were conducted on 22RV1 cells, both with and without CHD9 knockdown. In brief, 5 million cells underwent cross-linking with 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 125 mM glycine. Subsequently, the cell pellets were twice washed with cold PBS and resuspended in 300 μL of modified RIPA buffer (10 mM Tris-HCL, pH=8; 1 mM EDTA; 140 mM NaCl; 1% Triton X-100; 0.1% SDS; 0.1% sodium deoxycholate) supplemented with protease inhibitor. The resuspended pellet underwent sonication for 18 cycles (30s on, 30s off) at 4 °C using  Bioruptor (Diagenode).
The purified DNA was then subjected to Illumina ChIP-Seq library construction using the ThruPLEX DNA-seq kit (Takara, R400428).

tag: chip antibody

value: ab4729, Abcam


title: ATAC-Seq, shGFP, rep1


title: ChIP-H3K27ac, shGFP, rep2


title: ChIP-H3K27ac, shCHD9, rep1


title: 11_GEX


title: JT38_oligo

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

description: Hashtag Oligo

data_processing:
Transcriptome was mapped using 10X cellranger
HTO was mapped using GMM-demux
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Colon

growth_protocol: MCF7 parental and MCF7 with ESR1 mutation (MCF-7.S1) were cultured in RPMI-1640, 10% FBS, 2mM L-Glutamine in 96 well format

extract_protocol:
Treatments were hashed with lipid modified oligos before single-cell RNA-seq was performed using the Chromium Single Cell 3' kit (V3.1) from 10X Genomics
Library was constructed with 10x Genomics, Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: Wells were treated at 96 or 24 hours before collection for single cell sequencing with DMSO; Palbociclib ; Giredestrant ; Inavolisib ; Palbociclib/Giredestrant ; Palbociclib/Inavolisib ; Giredestrant/Inavolisib; Palbo/Giredestrant/Inavolisib at 200nM.

value: Colon


title: ChIP-CHD9, shGFP, rep2

value: 13402-1-AP, Proteintech


title: JT36_oligo

description: Hashtag Oligo


title: ChIP-CHD9, shCHD9, rep1


title: JT38


title: ChIP-H3K27ac, shGFP, rep1


title: JT37


title: JT37_oligo

description: Hashtag Oligo


title: ChIP-CHD9, shGFP, rep1


title: 6_GEX

value: Hippocampal tissue


title: JT36


title: 7_GEX


title: LIB5440392_SAM24399188

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-11-1, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

source_name: Breast

growth_protocol: MCF7 parental and MCF7 with ESR1 mutation (MCF-7.S1) were cultured in RPMI-1640, 10% FBS, 2mM L-Glutamine

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Mini kit (Cat. No. 74034),
For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: Cells were treated as annotated for 24 or 96 hours

value: Breast

tag: treatment


title: LIB5440390_SAM24399186


title: LIB5440391_SAM24399187


title: LIB5440394_SAM24399190


title: LIB5440389_SAM24399185


title: LIB5440388_SAM24399184


title: LIB5440387_SAM24399183


title: LIB5440385_SAM24399181


title: LIB5440383_SAM24399179


title: LIB5440384_SAM24399180


title: LIB5440382_SAM24399178


title: LIB5440386_SAM24399182


title: ChIP-CHD9, shCHD9, rep2


title: LIB5440379_SAM24399175


title: LIB5440380_SAM24399176


title: LIB5440381_SAM24399177


title: LIB5440378_SAM24399174


title: LIB5440377_SAM24399173


title: LIB5440376_SAM24399172


title: LIB5440375_SAM24399171


title: LIB5440372_SAM24399168


title: LIB5440374_SAM24399170


title: LIB5440373_SAM24399169


title: LIB5440371_SAM24399167


title: LIB5440369_SAM24399165


title: LIB5440393_SAM24399189


title: LIB5440368_SAM24399164


title: LIB5440366_SAM24399162


title: LIB5440367_SAM24399163


title: LIB5440365_SAM24399161


title: LIB5440363_SAM24399159


title: LIB5440364_SAM24399160


title: LIB5440362_SAM24399158


title: LIB5440361_SAM24399157


title: LIB5440358_SAM24399154


title: LIB5440360_SAM24399156


title: LIB5440359_SAM24399155


title: LIB5440356_SAM24399152


title: LIB5440357_SAM24399153


title: LIB5440355_SAM24399151


title: LIB5440354_SAM24399150


title: LIB5440350_SAM24399146


title: LIB5440352_SAM24399148


title: LIB5440351_SAM24399147


title: LIB5440353_SAM24399149


title: LIB5440349_SAM24399145


title: LIB5440370_SAM24399166


title: LIB5440348_SAM24399144


title: LIB5440344_SAM24399140


title: LIB5440343_SAM24399139


title: LIB5440346_SAM24399142


title: LIB5440345_SAM24399141


title: LIB5440341_SAM24399137


title: LIB5440340_SAM24399136


title: LIB5440338_SAM24399134


title: LIB5440339_SAM24399135


title: LIB5440333_SAM24399129


title: LIB5440336_SAM24399132


title: LIB5440335_SAM24399131


title: LIB5440334_SAM24399130


title: LIB5440332_SAM24399128


title: 22Rv1 cells, shCHD9_1_rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to hg38 by using STAR
Read counts were generated by STAR and the differential analysis was done by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: CHD9 knockdown

value: KD CHD9 by shRNA No.1


title: 22Rv1 cells, shCHD9_2_rep1

value: KD CHD9 by shRNA No.2


title: 22Rv1 cells, shCHD9_1_rep2


title: 22Rv1 cells, shCHD9_2_rep3


title: 22Rv1 cells, shCHD9_2_rep2


title: LIB5440347_SAM24399143


title: 22Rv1 cells, shGFP_rep2

value: WT

value: KD GFP


title: KA809YN6-09

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

description:
Quantstudio 7K Flex
JSAUG1R01_319

scan_protocol: Each card was assayed on a QuantStudio 7K Flex (Thermo Fisher) by automatic loading of the cards using an Orbitor R2 robot to increase throughput and to ensure that each participants matching CSF and plasma were assayed on the same day.

data_processing:
Wells were considered adequately measured if the AmpScore was ≥ 1 and the CqConf was ≥ 0.8. Wells that did not meet this standard ("acceptable QC") or were labeled "Undetermined" by QuantStudio were considered missing measurements, regardless of Cq value. Wells with acceptable QC but Cq > 34 (in CSF) or Cq > 35 (in plasma) were considered censored values and given special handling using censoring-aware methods in the analysis
miRNAs hsa-miR-499a-3p-478948 and hsa-miR-647-479126 were preselected as negative control probes and not expected to amplify with acceptable QC (see below) in any well; this was fulfilled in the data
The spike-in positive control miRNA cel-miR-39-3p-478293 and primary endogenous normalization reference control miRNA hsa-miR-16-5p-477860 were both required to be completely observed with acceptable QC in all wells for all samples; this was fulfilled in the data. Moreover, miRNAs hsa-miR-24-3p-477992, hsa-miR-92a-3p-477827, and hsa-miR-204-5p-478491 were preselected as positive control normalizer probes and expected to amplify with acceptable QC in at least 90% of wells and show no association with Alzheimer's disease status; this was also fulfilled in the data, with complete observation meeting acceptable QC for miR-24-3p and near-complete observation for miR-92a-3p (complete in plasma, 8% dropout in CSF) and miR-204-5p (4% dropout in plasma, 1% dropout in CSF)
32 (10% of 320) samples displaying one or more of three types of aberrant measurement profile were excluded for a final count of 288 samples (from 156 donors) in the study. The aberrant profile types were: 1) low miRNA yield associated with large or missing Cq values across the entire array (n=9; 2.8%), defined as > 15% missing Cq values; 2) an abnormal Cq distribution shift away from the cohort center of all miRNAs that was inconsistent with the spike-in measurements and suggested RNA concentration irregularities that occurred prior to the spike-in (n=17; 5.3%), defined as a divergence for the global median Cq of > 3.3 spike-in standard deviations from the spike-in median for the sample; and 3) large Cq values for spike-in wells only with no corresponding shift in the Cq values for the human miRNAs assayed (n=11; 3.4%), defined as a sample with a studentized residual > 2 and DFITS > 0.112 (= 2 x sqrt(1/320)) for the sample in a regression of the spike-in mean on the RT-qPCR run order. 4 of the 160 donors had both their CSF and plasma samples excluded by these criteria. The excluded samples were: JSAUG1R01_014 (CSF), JSAUG1R01_023 (Plasma), JSAUG1R01_026 (CSF), JSAUG1R01_033 (CSF), JSAUG1R01_040 (CSF) + JSAUG1R01_045 (Plasma) for donor 5275, JSAUG1R01_046 (Plasma), JSAUG1R01_082 (CSF), JSAUG1R01_091 (CSF) + JSAUG1R01_095 (Plasma) for donor 4802, JSAUG1R01_110 (CSF), JSAUG1R01_113 (Plasma) + JSAUG1R01_119 (CSF) for donor 4075, JSAUG1R01_116 (Plasma), JSAUG1R01_122 (CSF), JSAUG1R01_125 (Plasma), JSAUG1R01_126 (CSF), JSAUG1R01_127 (Plasma), JSAUG1R01_146 (CSF), JSAUG1R01_189 (Plasma), JSAUG1R01_191 (Plasma), JSAUG1R01_200 (CSF), JSAUG1R01_211 (CSF), JSAUG1R01_242 (CSF), JSAUG1R01_270 (Plasma), JSAUG1R01_280 (CSF), JSAUG1R01_282 (Plasma), JSAUG1R01_286 (Plasma), JSAUG1R01_304 (Plasma) + JSAUG1R01_308 (CSF) for donor 4598, JSAUG1R01_315 (Plasma), JSAUG1R01_320 (CSF)
Censored Cq values are viewed as quantitatively unreliable because their measurement falls outside the linear range of the assay, so we treated these as interval observations, defined as an unobserved value falling between an upper and a lower limit. Non-censored Cq values with acceptable QC were used as exact measurements (both bounds of the interval are the same normalized Cq value). Censored Cq values with acceptable QC were treated as falling between the biofluid-specific censoring threshold (lower bound) and the average (upper bound) of the normalized Cq value and the maximum normalized Cq value across all observations on all miRNAs (the "observed maximum", a value that will be strictly less than the maximum cycle number of 40, specified as a machine setting). Fully missing Cq values (marked as "Undetermined" by QuantStudio) were treated as falling between the observed maximum (lower bound) and the maximum cycle number (upper bound of 40). Non-missing Cq values with unacceptable QC were treated as missing measurements except that the recorded Cq (with all normalization adjustments; see value definition below) was used instead of the observed maximum as the lower bound. All the interval bounds were subtracted from the maximum cycle number of 40 to invert the Cq scale so that positive values mark higher expression
The triplicate wells for each sample for each miRNA were summarized into a single most-likely value on the expression (inverted normalized Cq) scale using a Bayesian multilevel interval regression model that considers all replicate wells for the sample jointly and naturally accounts for the different character of censored values in the context of non-censored values for the same miRNA when making predictions. For the Bayesian prior distribution on the biofluid-specific mean level for the miRNA we used a Student's t distribution with 4 degrees of freedom and a (wide and uninformative) scale of 10, and for the log of the root mean square error we used a (similarly uninformative) half-Cauchy distribution with the same scale of 10. Random effects for individual samples were assigned a zero-centered prior normal distribution with default conjugate inverse-gamma hyperprior (shape and scale parameters both 1/100) for the random-effect variance. The imputed value for a missing or censored observation was taken as the posterior biofluid-specific grand mean for the miRNA plus the posterior mean of the random effect, based on 10000 Markov chain Monte Carlo draws from the posterior distribution, following a burn-in run of 2500 draws. Note that the rank correlation between the predictions from this model and the naïve means of the corresponding replicate wells was 0.99, reflecting almost complete preservation of rank ordering among samples, but the model prediction is less biased because it accounts for censoring, which prevents it from overestimating the expression level. This bias correction was very necessary for CSF, where censoring was common, but less so for plasma, which had only small amounts of censoring
Cq measurement variance caused by RNA isolation variance was adjusted via median-alignment of the cel-miR-39-3p-478293 spike‑in control reactions as an exogenous calibration factor .For further endogenous calibration of Cq distributions across samples we identified 17 miRNAs in CSF and 53 in plasma that were always present with acceptable QC in 100% of the samples and used these to align the Cq distributions across all donors. For each biofluid, we calculated the median over the per-biofluid always-observed miRNAs and modeled both biofluid medians as a function of a 7-knot restricted cubic spline of the RT-qPCR run order using a linear mixed-effects regression model including random intercepts per donor. Residuals from this model were subtracted from the corresponding Cq values for all miRNAs to align the Cq distributions across all donors. Following this, batch calibration was performed to remove residual technical artifacts in the Cq measurements attributable to processing order. Each paired biofluid RNA (CSF and plasma from same donor) was run on separate cards (to ensure appropriate thresholding and baselining for each biofluid separately) but on the same day to minimize any potential batch effects, so order-related processing effects were expected to affect both biofluids similarly. To account for these, biofluid differences were subtracted out using an absorbing linear regression, which enforced a grand mean of zero across the Cq distribution, and then we fit a linear mixed-effects regression model including the same 7-knot restricted cubic spline of the RT-qPCR run order as above, interacted with a biofluid selector to allow for biofluid-specific adjustments to the fit, and additionally including indicators for known abnormal events or conditions noted during processing, with isolation batches entered as random intercepts. Fitted values from this regression were subtracted from the corresponding Cq values for all miRNAs as the adjustment for batch and order-related effects. Finally, we performed a Cq normalization using a mixed-effects model on the endogenous miRNA normalizer (hsa-miR-16-5p-477860, hsa-miR-24-3p-477992, hsa-miR-92a-3p-477827, and hsa-miR-204-5p-478491) Cq values only. The model included quadratic effects of age, fully-interacted indicators for sex and AD diagnosis , and crossed random effects to model the miRNA-sample interaction. We used this model to estimate the residual differences between different samples (irrespective of biofluid) as BLUPs (best linear unbiased predictions); the BLUP values were subtracted from the fully calibrated Cq values as endogenous normalizer level effects across samples, normalizing the Cq values to those levels. Note that the two biofluids are also normalized by this step, so that miRNA expression is now relative to the normalizer specific to each biofluid. The resulting normalized Cq values were then recentered to the global median of the input Cq value distribution

label: FAM

source_name: Cerebral Spinal Fluid

label_protocol: MiRNA was converted to cDNA using the TaqMan Advanced miRNA cDNA Synthesis kit (A28007, Thermo Fisher). 3 μL of RNA was 3’ poly-adenylated, followed by a 5’ adaptor ligation step and reverse transcription (RT). 5 μL of the RT mix was added to a 14 cycle universal miR-amplification step (miR-amp). The miR-amp reaction was diluted 1:10 with nuclease free water, then 110 μL of the diluted cDNA was mixed with 220 μL of TaqMan Fast Advanced master mix (4444556, Thermo Fisher) and 110 μL of nuclease free water. 100 μL of the qPCR mix from one sample was loaded into the first 4 ports of a 384-well custom TaqMan Advanced Human miRNA Card (Thermo Fisher), then 100 μL of the qPCR mix from a second sample was loaded into the last 4 ports.

extract_protocol: Each RNA isolation batch consisted of 24 samples processed on the same day: 12 pairs of donor- and date-matched CSF and plasma samples, grouped to keep individual donor samples together to avoid any potential effect due to RNA isolation batch. Biofluid samples were thawed on ice and total RNA was isolated from 250 μL of CSF and 250 μL of plasma using the Urine miRNA Purification kit (Norgen, Thorold, ON) following the manufacturers protocol. Following addition of lysis buffer to the sample, an exogenous cel-miR-39-3p spike-in (Thermo Fisher, Waltham, MA) was added at a final concentration of 3 pM. CSF and plasma RNA were eluted with 30 μL and 50 μL of nuclease free water, respectively. The miRNA concentration of each sample was measured using the Qubit miRNA Assay kit (Thermo Fisher) and read using a Qubit 4.0 fluorometer (Thermo Fisher).

tag: donor id

tag: subject status

value: Alzheimer's Disease

tag: Sex

value: Male

tag: age

tag: anatomical location

value: Structure of nervous tissue

tag: sample collection method

value: Lumbar Puncture

value: Cerebral Spinal Fluid

tag: starting amount

tag: holding temperature

tag: molecule type

value: total cell-free biofluid RNA


title: 22Rv1 cells, shGFP_rep1

tag: cell line

value: human prostate cancer


title: AA8088RV-11

description:
Quantstudio 7K Flex
JSAUG1R01_317

value: Healthy Control

tag: tissue


title: 22Rv1 cells, shGFP_rep3


title: JA808RKS-11

description:
Quantstudio 7K Flex
JSAUG1R01_318

source_name: Plasma

value: Female

value: Circulating blood

value: Venous

value: Plasma


title: GA80B4B8-02

description:
Quantstudio 7K Flex
JSAUG1R01_316


title: BA8081QL-07

description:
Quantstudio 7K Flex
JSAUG1R01_315


title: LIB5440331_SAM24399127

value: Breast


title: FA807WT2-11

description:
Quantstudio 7K Flex
JSAUG1R01_320


title: 22Rv1 cells, shCHD9_1_rep1

value: CHD9 knockdown

value: KD CHD9 by shRNA No.1


title: GA80B8KK-02

description:
Quantstudio 7K Flex
JSAUG1R01_312


title: LIB5440342_SAM24399138


title: EA808TJ2-10

description:
Quantstudio 7K Flex
JSAUG1R01_314


title: LIB5440337_SAM24399133


title: CA80975P-01

description:
Quantstudio 7K Flex
JSAUG1R01_310


title: AA809MN7-08

description:
Quantstudio 7K Flex
JSAUG1R01_311


title: EA807NX8-07

description:
Quantstudio 7K Flex
JSAUG1R01_313


title: CA807QDJ-08

description:
Quantstudio 7K Flex
JSAUG1R01_309


title: BA8094C6-09

description:
Quantstudio 7K Flex
JSAUG1R01_308


title: CA809KGT-09

description:
Quantstudio 7K Flex
JSAUG1R01_306


title: JA808Q9V-04

description:
Quantstudio 7K Flex
JSAUG1R01_304


title: HA809886-02

description:
Quantstudio 7K Flex
JSAUG1R01_303


title: KA809D8F-09

description:
Quantstudio 7K Flex
JSAUG1R01_302


title: FA807T0C-06

description:
Quantstudio 7K Flex
JSAUG1R01_300


title: JA80981M-07

description:
Quantstudio 7K Flex
JSAUG1R01_299


title: 35dpf_mut_3

city: Sagamihara

first: Kota

last: Ujibe

address: 5-10-1, Fuchinobe, Chuo-ku

country: Japan

institute: Aoyama Gakuin University

description:
RNA from single juvenile at mRNA
DrUji3-133

data_processing:
Mapping and gene quantification was descrived as previous (Kashima et al., 2021). In brief, only read 1 reads were processed with fastp (version 0.21.0)(Chen et al., 2018). The trimmed reads were then mapped to the zebrafish reference sequences ofDanio_rerio.GRCz11.101 using BWA-MEM (version 0.7.17-r1188) (Li and Durbin, 2009)with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0)(Patro et al., 2017).
Assembly: Danio_rerio.GRCz11.cdna.all.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each Sample

organism: Danio rerio

source_name: whole organism

growth_protocol: Zebrafish (Danio rerio) were reared and maintained in 1.7 L tanks in a recirculating Meito System (Meito System) under a 14 h light and 10 h dark photoperiod according to the standard protocol.

extract_protocol:
RNA extraction from larvae and juvenile zebrafish and RNA purification were described as previous(Ujibe et al., 2021). In brief, RNA extraction from 4-12 dpf larvae was conducted by vortexing sample and TRI-reagent LS (Molecular Research Center) in an 8-strip tube for 1 min at RT. RNA extraction from 15-35 dpf larvae/juveniles was conducted by homogenizing samples in TRI-reagent LS using BioMasherⅡ (Nippi) for 1 min at RT. Equal amounts of 99.5% Ethanol was added to RNA lysates and mixed. The mixtures were applied to AcroPrep Advance 96-well Long Tip Filter Plate for Nucleic Acid Binding (Pall) and centrifuged at 1,300 x g for 4 min at RT. The RNA adsorbed by the filter was washed twice with 99.5% Ethanol and once with 80% Ethanol and finally eluted with nuclease-free water.
Library preparation was conducted according to the Lasy-Seq ver 1.1 method. In brief, reverse transcription was done using SuperScript IV reverse transcriptase (Thermo Fisher Scientific) and indexed reverse transcription primers. Following program was used for reverse transcription: 65 °C 10 min; 80 °C 15 min; 4 °C forever in ProFlex PCR System. Products of reverse transcription were pooled and then purified using an equal volume of AMpure XP beads (Beckman Coulter) according to the manufacturer’s manual. Second strand synthesis was conducted with RNaseH (Enzymatics) and DNA polymerase I (Enzymatics) at 16 °C for 2 h. Synthetic double-strand DNA (dsDNA) were treated with RNase T1 (Thermo Fisher Scientific) at 37 °C for 5 min. Fragmentation was conducted using 5x WGS Fragmentation Mix (Enzymatics) at 32 °C for 6.5 min followed by heat inactivation at 65 °C for 30 min. Ligation was conducted using 5x Ligation Mix (Enzymatics) at 20 °C for 15 min. Library amplification was conducted using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS) using the following program: 95 °C 5 min; 98 °C 20 s, 60 °C 15 s, 72 °C 40 s, 12 cycles; 72 °C 3 min; 4 °C forever in QuantStudio 5 Real-Time PCR Systems (Thermo Fisher Scientific). The library was subjected to electrophoresis using Bioanalyzer 2,100 (Agilent Technologies) with the Agilent High Sensitivity DNA kit (Agilent Technologies) according to the manufacturer’s manual. Library concentration was determined using Quantus Fluorometer (Promega) with the QuantiFluor ONE dsDNA System kit (Promega) and diluted to 4 ng/µl. Sequencing of 150-bp paired-end reads was conducted using HiSeq X Ten (Illumina).

value: whole organism

tag: developmental stage

value: mutant


title: 35dpf_mut_4

description:
RNA from single juvenile at mRNA
DrUji3-134


title: DA809PN9-02

description:
Quantstudio 7K Flex
JSAUG1R01_298

value: Alzheimer's Disease


title: DA807HF1-08

description:
Quantstudio 7K Flex
JSAUG1R01_297

value: Male


title: 35dpf_mut_1

description:
RNA from single juvenile at mRNA
DrUji3-131


title: CA809WBK-02

description:
Quantstudio 7K Flex
JSAUG1R01_294


title: FA809R46-08

description:
Quantstudio 7K Flex
JSAUG1R01_295

value: Structure of nervous tissue


title: HA8098JD-02

description:
Quantstudio 7K Flex
JSAUG1R01_296


title: 35dpf_mut_2

description:
RNA from single juvenile at mRNA
DrUji3-132


title: 35dpf_WT_4

description:
RNA from single juvenile at mRNA
DrUji3-128

value: wild-type


title: AA809XGZ-09

description:
Quantstudio 7K Flex
JSAUG1R01_292

value: Lumbar Puncture

value: Cerebral Spinal Fluid


title: 35dpf_WT_5

description:
RNA from single juvenile at mRNA
DrUji3-129


title: KA809X3Q-10

description:
Quantstudio 7K Flex
JSAUG1R01_293

value: total cell-free biofluid RNA


title: 35dpf_WT_6

description:
RNA from single juvenile at mRNA
DrUji3-130


title: 35dpf_WT_3

description:
RNA from single juvenile at mRNA
DrUji3-127


title: 35dpf_WT_2

description:
RNA from single juvenile at mRNA
DrUji3-126


title: 35dpf_WT_1

description:
RNA from single juvenile at mRNA
DrUji3-125


title: JA809ZTR-12

description:
Quantstudio 7K Flex
JSAUG1R01_307

value: Healthy Control


title: CA807CDR-03

description:
Quantstudio 7K Flex
JSAUG1R01_291


title: JA808VB8-05

description:
Quantstudio 7K Flex
JSAUG1R01_305

value: Female


title: BA807RZN-08

description:
Quantstudio 7K Flex
JSAUG1R01_289


title: CA809FGN-03

description:
Quantstudio 7K Flex
JSAUG1R01_290

value: Circulating blood


title: 28dpf_mut_12

description:
RNA from single juvenile at mRNA
DrUji3-124


title: 28dpf_mut_11

description:
RNA from single juvenile at mRNA
DrUji3-123


title: FA80CJ27-08

description:
Quantstudio 7K Flex
JSAUG1R01_288


title: BA8076BX-02

description:
Quantstudio 7K Flex
JSAUG1R01_301

value: Venous


title: AA808DXV-09

description:
Quantstudio 7K Flex
JSAUG1R01_287


title: 28dpf_mut_9

description:
RNA from single juvenile at mRNA
DrUji3-121


title: BA80860F-08

description:
Quantstudio 7K Flex
JSAUG1R01_286

value: Plasma


title: GA809XXL-10

description:
Quantstudio 7K Flex
JSAUG1R01_285


title: 28dpf_mut_8

description:
RNA from single juvenile at mRNA
DrUji3-120


title: 28dpf_mut_7

description:
RNA from single juvenile at mRNA
DrUji3-119


title: CA807GZ8-14

description:
Quantstudio 7K Flex
JSAUG1R01_283


title: CA80C2NF-02

description:
Quantstudio 7K Flex
JSAUG1R01_282


title: EA808744-02

description:
Quantstudio 7K Flex
JSAUG1R01_281


title: 28dpf_mut_5

description:
RNA from single juvenile at mRNA
DrUji3-117


title: 28dpf_mut_6

description:
RNA from single juvenile at mRNA
DrUji3-118


title: HA809W3T-09

description:
Quantstudio 7K Flex
JSAUG1R01_280


title: DA809W9M-02

description:
Quantstudio 7K Flex
JSAUG1R01_284


title: BA80B46S-02

description:
Quantstudio 7K Flex
JSAUG1R01_278


title: 28dpf_mut_3

description:
RNA from single juvenile at mRNA
DrUji3-115


title: 28dpf_mut_1

description:
RNA from single juvenile at mRNA
DrUji3-113


title: 28dpf_mut_4

description:
RNA from single juvenile at mRNA
DrUji3-116


title: EA8077RX-04

description:
Quantstudio 7K Flex
JSAUG1R01_279


title: BA808B3R-10

description:
Quantstudio 7K Flex
JSAUG1R01_277


title: 28dpf_WT_6

description:
RNA from single juvenile at mRNA
DrUji3-112


title: 28dpf_mut_2

description:
RNA from single juvenile at mRNA
DrUji3-114


title: HA809LZZ-10

description:
Quantstudio 7K Flex
JSAUG1R01_276


title: 28dpf_WT_5

description:
RNA from single juvenile at mRNA
DrUji3-111


title: DA8099RB-07

description:
Quantstudio 7K Flex
JSAUG1R01_275


title: DA80816L-09

description:
Quantstudio 7K Flex
JSAUG1R01_274


title: 28dpf_WT_3

description:
RNA from single juvenile at mRNA
DrUji3-109


title: 28dpf_WT_2

description:
RNA from single juvenile at mRNA
DrUji3-108


title: DA8083YH-03

description:
Quantstudio 7K Flex
JSAUG1R01_273


title: 28dpf_mut_10

description:
RNA from single juvenile at mRNA
DrUji3-122


title: 28dpf_WT_1

description:
RNA from single juvenile at mRNA
DrUji3-107


title: KA807K8L-03

description:
Quantstudio 7K Flex
JSAUG1R01_270


title: 9dpf_mut_10

description:
RNA from single larva at mRNA
DrUji3-106


title: KA809LYX-09

description:
Quantstudio 7K Flex
JSAUG1R01_271


title: 9dpf_mut_9

description:
RNA from single larva at mRNA
DrUji3-105


title: GA809WFJ-02

description:
Quantstudio 7K Flex
JSAUG1R01_269


title: EA808J9G-08

description:
Quantstudio 7K Flex
JSAUG1R01_268


title: 9dpf_mut_7

description:
RNA from single larva at mRNA
DrUji3-103


title: 9dpf_mut_8

description:
RNA from single larva at mRNA
DrUji3-104


title: FA809V8X-07

description:
Quantstudio 7K Flex
JSAUG1R01_266


title: HA808K29-10

description:
Quantstudio 7K Flex
JSAUG1R01_265


title: FA8099ZS-10

description:
Quantstudio 7K Flex
JSAUG1R01_267


title: DA80C5SK-03

description:
Quantstudio 7K Flex
JSAUG1R01_264


title: 9dpf_mut_5

description:
RNA from single larva at mRNA
DrUji3-101


title: 28dpf_WT_4

description:
RNA from single juvenile at mRNA
DrUji3-110


title: 9dpf_mut_4

description:
RNA from single larva at mRNA
DrUji3-96


title: EA808DCK-11

description:
Quantstudio 7K Flex
JSAUG1R01_263


title: EA807ZPB-12

description:
Quantstudio 7K Flex
JSAUG1R01_262


title: 9dpf_mut_3

description:
RNA from single larva at mRNA
DrUji3-95


title: 9dpf_WT_6

description:
RNA from single larva at mRNA
DrUji3-92


title: BA807MG3-07

description:
Quantstudio 7K Flex
JSAUG1R01_260


title: 9dpf_mut_1

description:
RNA from single larva at mRNA
DrUji3-93


title: KA809CSP-09

description:
Quantstudio 7K Flex
JSAUG1R01_259


title: 9dpf_mut_2

description:
RNA from single larva at mRNA
DrUji3-94


title: 9dpf_WT_4

description:
RNA from single larva at mRNA
DrUji3-90


title: HA808P75-06

description:
Quantstudio 7K Flex
JSAUG1R01_272


title: 9dpf_WT_3

description:
RNA from single larva at mRNA
DrUji3-89


title: BA807TTB-11

description:
Quantstudio 7K Flex
JSAUG1R01_257


title: GA8086KX-14

description:
Quantstudio 7K Flex
JSAUG1R01_256


title: 9dpf_WT_1

description:
RNA from single larva at mRNA
DrUji3-87


title: 9dpf_WT_2

description:
RNA from single larva at mRNA
DrUji3-88


title: 9dpf_mut_6

description:
RNA from single larva at mRNA
DrUji3-102


title: 8dpf_mut_14

description:
RNA from single larva at mRNA
DrUji3-86


title: KA808FWK-09

description:
Quantstudio 7K Flex
JSAUG1R01_254


title: 8dpf_mut_12

description:
RNA from single larva at mRNA
DrUji3-84


title: KA808BG5-03

description:
Quantstudio 7K Flex
JSAUG1R01_252


title: 8dpf_mut_11

description:
RNA from single larva at mRNA
DrUji3-83


title: 8dpf_mut_9

description:
RNA from single larva at mRNA
DrUji3-81


title: 8dpf_mut_10

description:
RNA from single larva at mRNA
DrUji3-82


title: KA80CK45-08

description:
Quantstudio 7K Flex
JSAUG1R01_253


title: BA808B1P-10

description:
Quantstudio 7K Flex
JSAUG1R01_249


title: 8dpf_mut_8

description:
RNA from single larva at mRNA
DrUji3-80


title: EA80CL29-08

description:
Quantstudio 7K Flex
JSAUG1R01_251


title: DA808Q3Z-10

description:
Quantstudio 7K Flex
JSAUG1R01_250


title: 8dpf_mut_5

description:
RNA from single larva at mRNA
DrUji3-77


title: FA80B8MN-04

description:
Quantstudio 7K Flex
JSAUG1R01_248


title: 8dpf_mut_7

description:
RNA from single larva at mRNA
DrUji3-79


title: JA808SQW-10

description:
Quantstudio 7K Flex
JSAUG1R01_247


title: 8dpf_mut_4

description:
RNA from single larva at mRNA
DrUji3-76


title: GA80743R-04

description:
Quantstudio 7K Flex
JSAUG1R01_258


title: 9dpf_WT_5

description:
RNA from single larva at mRNA
DrUji3-91


title: KA80762R-11

description:
Quantstudio 7K Flex
JSAUG1R01_261


title: KA8091CZ-02

description:
Quantstudio 7K Flex
JSAUG1R01_245


title: AA80865X-04

description:
Quantstudio 7K Flex
JSAUG1R01_243


title: 8dpf_mut_3

description:
RNA from single larva at mRNA
DrUji3-75


title: KA808S6T-02

description:
Quantstudio 7K Flex
JSAUG1R01_255


title: EA80C4M9-02

description:
Quantstudio 7K Flex
JSAUG1R01_246


title: 8dpf_mut_2

description:
RNA from single larva at mRNA
DrUji3-74


title: 8dpf_mut_13

description:
RNA from single larva at mRNA
DrUji3-85


title: 8dpf_mut_1

description:
RNA from single larva at mRNA
DrUji3-73


title: BA808BW8-11

description:
Quantstudio 7K Flex
JSAUG1R01_242


title: 8dpf_WT_6

description:
RNA from single larva at mRNA
DrUji3-72


title: HA809NKD-08

description:
Quantstudio 7K Flex
JSAUG1R01_241


title: 8dpf_WT_5

description:
RNA from single larva at mRNA
DrUji3-71


title: HA809BZF-01

description:
Quantstudio 7K Flex
JSAUG1R01_240


title: HA80BCPC-03

description:
Quantstudio 7K Flex
JSAUG1R01_239


title: 8dpf_WT_4

description:
RNA from single larva at mRNA
DrUji3-70


title: 8dpf_mut_6

description:
RNA from single larva at mRNA
DrUji3-78


title: 8dpf_WT_3

description:
RNA from single larva at mRNA
DrUji3-69


title: 8dpf_WT_2

description:
RNA from single larva at mRNA
DrUji3-68


title: AA808J1S-04

description:
Quantstudio 7K Flex
JSAUG1R01_236


title: CA809RCL-10

description:
Quantstudio 7K Flex
JSAUG1R01_237


title: 8dpf_WT_1

description:
RNA from single larva at mRNA
DrUji3-67


title: FA80BCHL-08

description:
Quantstudio 7K Flex
JSAUG1R01_235


title: 7dpf_mut_13

description:
RNA from single larva at mRNA
DrUji3-66


title: JA80BDM0-09

description:
Quantstudio 7K Flex
JSAUG1R01_234


title: 7dpf_mut_12

description:
RNA from single larva at mRNA
DrUji3-65


title: BA80B04B-08

description:
Quantstudio 7K Flex
JSAUG1R01_244


title: 7dpf_mut_11

description:
RNA from single larva at mRNA
DrUji3-64


title: DA808HYH-11

description:
Quantstudio 7K Flex
JSAUG1R01_233


title: FA80BN4V-02

description:
Quantstudio 7K Flex
JSAUG1R01_232


title: BA809MVG-09

description:
Quantstudio 7K Flex
JSAUG1R01_231


title: 7dpf_mut_10

description:
RNA from single larva at mRNA
DrUji3-63


title: 7dpf_mut_9

description:
RNA from single larva at mRNA
DrUji3-62


title: BA807J7L-07

description:
Quantstudio 7K Flex
JSAUG1R01_230


title: 7dpf_mut_8

description:
RNA from single larva at mRNA
DrUji3-61


title: 7dpf_mut_6

description:
RNA from single larva at mRNA
DrUji3-59


title: EA8096MW-08

description:
Quantstudio 7K Flex
JSAUG1R01_228


title: CA8098LK-02

description:
Quantstudio 7K Flex
JSAUG1R01_229


title: 7dpf_mut_4

description:
RNA from single larva at mRNA
DrUji3-57


title: 7dpf_mut_5

description:
RNA from single larva at mRNA
DrUji3-58


title: DA807DT3-09

description:
Quantstudio 7K Flex
JSAUG1R01_238


title: GA8082S2-07

description:
Quantstudio 7K Flex
JSAUG1R01_227


title: DA808WLF-02

description:
Quantstudio 7K Flex
JSAUG1R01_225


title: AA80B402-03

description:
Quantstudio 7K Flex
JSAUG1R01_224


title: 7dpf_mut_2

description:
RNA from single larva at mRNA
DrUji3-55


title: 7dpf_mut_1

description:
RNA from single larva at mRNA
DrUji3-54


title: HA807M9C-03

description:
Quantstudio 7K Flex
JSAUG1R01_222


title: EA8087XD-09

description:
Quantstudio 7K Flex
JSAUG1R01_223


title: AA8097FQ-02

description:
Quantstudio 7K Flex
JSAUG1R01_221


title: 7dpf_WT_5

description:
RNA from single larva at mRNA
DrUji3-52


title: 7dpf_WT_6

description:
RNA from single larva at mRNA
DrUji3-53


title: GA8088T9-09

description:
Quantstudio 7K Flex
JSAUG1R01_220


title: 7dpf_WT_4

description:
RNA from single larva at mRNA
DrUji3-51


title: JA8083ZS-02

description:
Quantstudio 7K Flex
JSAUG1R01_219


title: 7dpf_WT_3

description:
RNA from single larva at mRNA
DrUji3-50


title: 7dpf_WT_2

description:
RNA from single larva at mRNA
DrUji3-49


title: KA807X0Z-08

description:
Quantstudio 7K Flex
JSAUG1R01_218


title: 6dpf_mut_11

description:
RNA from single larva at mRNA
DrUji3-47


title: 7dpf_WT_1

description:
RNA from single larva at mRNA
DrUji3-48


title: CA80B8QV-07

description:
Quantstudio 7K Flex
JSAUG1R01_215


title: 6dpf_mut_10

description:
RNA from single larva at mRNA
DrUji3-46


title: 7dpf_mut_7

description:
RNA from single larva at mRNA
DrUji3-60


title: 6dpf_mut_9

description:
RNA from single larva at mRNA
DrUji3-45


title: FA8086MC-09

description:
Quantstudio 7K Flex
JSAUG1R01_214


title: JA809YWC-11

description:
Quantstudio 7K Flex
JSAUG1R01_226


title: DA807N7W-03

description:
Quantstudio 7K Flex
JSAUG1R01_212


title: 7dpf_mut_3

description:
RNA from single larva at mRNA
DrUji3-56


title: KA80JJX3-03

description:
Quantstudio 7K Flex
JSAUG1R01_213


title: JA80B3NV-10

description:
Quantstudio 7K Flex
JSAUG1R01_211


title: 6dpf_mut_7

description:
RNA from single larva at mRNA
DrUji3-43


title: 6dpf_mut_5

description:
RNA from single larva at mRNA
DrUji3-41


title: JA807NQL-10

description:
Quantstudio 7K Flex
JSAUG1R01_209


title: KA807PQW-05

description:
Quantstudio 7K Flex
JSAUG1R01_210


title: BA807HTM-13

description:
Quantstudio 7K Flex
JSAUG1R01_208


title: 6dpf_mut_4

description:
RNA from single larva at mRNA
DrUji3-40


title: 6dpf_mut_3

description:
RNA from single larva at mRNA
DrUji3-39


title: 6dpf_mut_1

description:
RNA from single larva at mRNA
DrUji3-37


title: 6dpf_mut_2

description:
RNA from single larva at mRNA
DrUji3-38


title: EA807X3D-03

description:
Quantstudio 7K Flex
JSAUG1R01_207


title: EA8082F9-07

description:
Quantstudio 7K Flex
JSAUG1R01_216


title: CA807W3X-10

description:
Quantstudio 7K Flex
JSAUG1R01_205


title: KA809K9M-06

description:
Quantstudio 7K Flex
JSAUG1R01_217


title: 6dpf_WT_5

description:
RNA from single larva at mRNA
DrUji3-35


title: 6dpf_WT_6

description:
RNA from single larva at mRNA
DrUji3-36


title: KA807WDG-10

description:
Quantstudio 7K Flex
JSAUG1R01_206


title: KA807V00-11

description:
Quantstudio 7K Flex
JSAUG1R01_203


title: 6dpf_WT_4

description:
RNA from single larva at mRNA
DrUji3-34


title: BA809Q11-02

description:
Quantstudio 7K Flex
JSAUG1R01_202


title: FA807TPX-04

description:
Quantstudio 7K Flex
JSAUG1R01_201


title: 6dpf_WT_2

description:
RNA from single larva at mRNA
DrUji3-32


title: 6dpf_WT_3

description:
RNA from single larva at mRNA
DrUji3-33


title: 6dpf_mut_8

description:
RNA from single larva at mRNA
DrUji3-44


title: 6dpf_WT_1

description:
RNA from single larva at mRNA
DrUji3-31


title: 6dpf_mut_6

description:
RNA from single larva at mRNA
DrUji3-42


title: DA809VFJ-09

description:
Quantstudio 7K Flex
JSAUG1R01_200


title: KA80978T-08

description:
Quantstudio 7K Flex
JSAUG1R01_199


title: DA808Y03-11

description:
Quantstudio 7K Flex
JSAUG1R01_198


title: 5dpf_mut_5

description:
RNA from single larva at mRNA
DrUji3-30


title: 5dpf_mut_4

description:
RNA from single larva at mRNA
DrUji3-29


title: 5dpf_mut_3

description:
RNA from single larva at mRNA
DrUji3-28


title: HA808T4F-08

description:
Quantstudio 7K Flex
JSAUG1R01_197


title: 5dpf_mut_1

description:
RNA from single larva at mRNA
DrUji3-26


title: JA8095VZ-02

description:
Quantstudio 7K Flex
JSAUG1R01_194


title: 5dpf_mut_2

description:
RNA from single larva at mRNA
DrUji3-27


title: 5dpf_WT_6

description:
RNA from single larva at mRNA
DrUji3-25


title: CA809YQV-09

description:
Quantstudio 7K Flex
JSAUG1R01_192


title: GA808Q05-04

description:
Quantstudio 7K Flex
JSAUG1R01_204


title: 5dpf_WT_4

description:
RNA from single larva at mRNA
DrUji3-23


title: 5dpf_WT_2

description:
RNA from single larva at mRNA
DrUji3-21


title: DA807MF1-07

description:
Quantstudio 7K Flex
JSAUG1R01_193


title: EA808HW5-09

description:
Quantstudio 7K Flex
JSAUG1R01_190


title: 5dpf_WT_3

description:
RNA from single larva at mRNA
DrUji3-22


title: JA80B4FK-02

description:
Quantstudio 7K Flex
JSAUG1R01_189


title: AA807PY3-02

description:
Quantstudio 7K Flex
JSAUG1R01_191


title: 5dpf_WT_5

description:
RNA from single larva at mRNA
DrUji3-24


title: DA8087TR-11

description:
Quantstudio 7K Flex
JSAUG1R01_187


title: 4dpf_mut_13

description:
RNA from single larva at mRNA
DrUji3-19


title: 5dpf_WT_1

description:
RNA from single larva at mRNA
DrUji3-20


title: 4dpf_mut_11

description:
RNA from single larva at mRNA
DrUji3-17


title: HA808BXL-10

description:
Quantstudio 7K Flex
JSAUG1R01_188


title: 4dpf_mut_12

description:
RNA from single larva at mRNA
DrUji3-18


title: 4dpf_mut_10

description:
RNA from single larva at mRNA
DrUji3-16


title: 4dpf_mut_9

description:
RNA from single larva at mRNA
DrUji3-15


title: DA809JWQ-08

description:
Quantstudio 7K Flex
JSAUG1R01_186


title: GA8082T7-12

description:
Quantstudio 7K Flex
JSAUG1R01_196


title: 4dpf_mut_8

description:
RNA from single larva at mRNA
DrUji3-14


title: EA809CWR-13

description:
Quantstudio 7K Flex
JSAUG1R01_195


title: DA807WCQ-10

description:
Quantstudio 7K Flex
JSAUG1R01_183


title: GA807W5Q-07

description:
Quantstudio 7K Flex
JSAUG1R01_184


title: HA8095SB-03

description:
Quantstudio 7K Flex
JSAUG1R01_181


title: 4dpf_mut_6

description:
RNA from single larva at mRNA
DrUji3-12


title: 4dpf_mut_7

description:
RNA from single larva at mRNA
DrUji3-13


title: GA8095LS-03

description:
Quantstudio 7K Flex
JSAUG1R01_180


title: 4dpf_mut_4

description:
RNA from single larva at mRNA
DrUji3-10


title: EA8091JC-02

description:
Quantstudio 7K Flex
JSAUG1R01_178


title: KA8082G5-09

description:
Quantstudio 7K Flex
JSAUG1R01_179


title: 4dpf_mut_5

description:
RNA from single larva at mRNA
DrUji3-11


title: CA80B8LJ-02

description:
Quantstudio 7K Flex
JSAUG1R01_177


title: 4dpf_mut_2

description:
RNA from single larva at mRNA
DrUji3-8


title: 4dpf_mut_3

description:
RNA from single larva at mRNA
DrUji3-9


title: DA809LHV-08

description:
Quantstudio 7K Flex
JSAUG1R01_176


title: 4dpf_mut_1

description:
RNA from single larva at mRNA
DrUji3-7


title: DA8097CM-08

description:
Quantstudio 7K Flex
JSAUG1R01_174


title: 4dpf_WT_5

description:
RNA from single larva at mRNA
DrUji3-5


title: 4dpf_WT_6

description:
RNA from single larva at mRNA
DrUji3-6


title: EA8077CV-03

description:
Quantstudio 7K Flex
JSAUG1R01_175


title: 4dpf_WT_4

description:
RNA from single larva at mRNA
DrUji3-4


title: AA8088Z7-05

description:
Quantstudio 7K Flex
JSAUG1R01_185


title: HA807YGP-03

description:
Quantstudio 7K Flex
JSAUG1R01_172


title: 4dpf_WT_3

description:
RNA from single larva at mRNA
DrUji3-3


title: FA80B03L-08

description:
Quantstudio 7K Flex
JSAUG1R01_171


title: 4dpf_WT_1

description:
RNA from single larva at mRNA
DrUji3-1


title: AA807Q87-03

description:
Quantstudio 7K Flex
JSAUG1R01_169


title: 4dpf_WT_2

description:
RNA from single larva at mRNA
DrUji3-2


title: AA807GHT-07

description:
Quantstudio 7K Flex
JSAUG1R01_170


title: 21dpf_mut_8

description:
RNA from single juvenile at mRNA
DreUjiNishi-365


title: FA808BM7-08

description:
Quantstudio 7K Flex
JSAUG1R01_182


title: HA807FQT-10

description:
Quantstudio 7K Flex
JSAUG1R01_167


title: 21dpf_mut_6

description:
RNA from single juvenile at mRNA
DreUjiNishi-363


title: 21dpf_mut_5

description:
RNA from single juvenile at mRNA
DreUjiNishi-362


title: HA807726-04

description:
Quantstudio 7K Flex
JSAUG1R01_168


title: 21dpf_mut_7

description:
RNA from single juvenile at mRNA
DreUjiNishi-364


title: EA80B3RT-02

description:
Quantstudio 7K Flex
JSAUG1R01_166


title: 21dpf_mut_3

description:
RNA from single juvenile at mRNA
DreUjiNishi-360


title: 21dpf_mut_4

description:
RNA from single juvenile at mRNA
DreUjiNishi-361


title: BA80C2MC-03

description:
Quantstudio 7K Flex
JSAUG1R01_162


title: EA807HQQ-10

description:
Quantstudio 7K Flex
JSAUG1R01_163


title: 21dpf_mut_2

description:
RNA from single juvenile at mRNA
DreUjiNishi-359


title: 21dpf_mut_1

description:
RNA from single juvenile at mRNA
DreUjiNishi-358


title: KA8081GK-06

description:
Quantstudio 7K Flex
JSAUG1R01_164


title: KA8080SS-11

description:
Quantstudio 7K Flex
JSAUG1R01_161


title: 21dpf_WT_5

description:
RNA from single juvenile at mRNA
DreUjiNishi-356


title: FA80CHJ3-08

description:
Quantstudio 7K Flex
JSAUG1R01_165


title: HA8071LZ-02

description:
Quantstudio 7K Flex
JSAUG1R01_159


title: DA807G7V-12

description:
Quantstudio 7K Flex
JSAUG1R01_160


title: 21dpf_WT_4

description:
RNA from single juvenile at mRNA
DreUjiNishi-355


title: DA809YF9-08

description:
Quantstudio 7K Flex
JSAUG1R01_158


title: DA8081JR-10

description:
Quantstudio 7K Flex
JSAUG1R01_173


title: AA807815-04

description:
Quantstudio 7K Flex
JSAUG1R01_157


title: HA80B8JT-02

description:
Quantstudio 7K Flex
JSAUG1R01_155


title: KA808XLD-06

description:
Quantstudio 7K Flex
JSAUG1R01_156


title: 21dpf_WT_1

description:
RNA from single juvenile at mRNA
DreUjiNishi-352


title: 21dpf_WT_2

description:
RNA from single juvenile at mRNA
DreUjiNishi-353


title: 18dpf_mut_2

description:
RNA from single larva at mRNA
DreUjiNishi-350


title: BA808Y8R-07

description:
Quantstudio 7K Flex
JSAUG1R01_154


title: KA80B4JJ-02

description:
Quantstudio 7K Flex
JSAUG1R01_152


title: BA80CRSJ-03

description:
Quantstudio 7K Flex
JSAUG1R01_153


title: 18dpf_WT_6

description:
RNA from single larva at mRNA
DreUjiNishi-348


title: 18dpf_WT_5

description:
RNA from single larva at mRNA
DreUjiNishi-347


title: 18dpf_mut_1

description:
RNA from single larva at mRNA
DreUjiNishi-349


title: EA809ZW3-08

description:
Quantstudio 7K Flex
JSAUG1R01_151


title: HA808SG1-02

description:
Quantstudio 7K Flex
JSAUG1R01_148


title: 18dpf_WT_3

description:
RNA from single larva at mRNA
DreUjiNishi-345


title: EA809YRJ-10

description:
Quantstudio 7K Flex
JSAUG1R01_149


title: 18dpf_WT_2

description:
RNA from single larva at mRNA
DreUjiNishi-344


title: JA808WYQ-03

description:
Quantstudio 7K Flex
JSAUG1R01_147


title: 21dpf_WT_6

description:
RNA from single juvenile at mRNA
DreUjiNishi-357


title: 15dpf_mut_6

description:
RNA from single larva at mRNA
DreUjiNishi-342


title: FA809FHM-02

description:
Quantstudio 7K Flex
JSAUG1R01_150


title: HA80D3MD-08

description:
Quantstudio 7K Flex
JSAUG1R01_146


title: 21dpf_WT_3

description:
RNA from single juvenile at mRNA
DreUjiNishi-354


title: 15dpf_mut_5

description:
RNA from single larva at mRNA
DreUjiNishi-341


title: 18dpf_WT_1

description:
RNA from single larva at mRNA
DreUjiNishi-343


title: JA80D225-08

description:
Quantstudio 7K Flex
JSAUG1R01_144


title: 18dpf_mut_3

description:
RNA from single larva at mRNA
DreUjiNishi-351


title: 15dpf_mut_3

description:
RNA from single larva at mRNA
DreUjiNishi-339


title: EA80D3N7-08

description:
Quantstudio 7K Flex
JSAUG1R01_143


title: 15dpf_mut_4

description:
RNA from single larva at mRNA
DreUjiNishi-340


title: CA809QJQ-08

description:
Quantstudio 7K Flex
JSAUG1R01_145


title: KA80CCDB-02

description:
Quantstudio 7K Flex
JSAUG1R01_141


title: 15dpf_mut_1

description:
RNA from single larva at mRNA
DreUjiNishi-337


title: 18dpf_WT_4

description:
RNA from single larva at mRNA
DreUjiNishi-346


title: GA809JXW-08

description:
Quantstudio 7K Flex
JSAUG1R01_140


title: FA8081SR-07

description:
Quantstudio 7K Flex
JSAUG1R01_138


title: 15dpf_mut_2

description:
RNA from single larva at mRNA
DreUjiNishi-338


title: 15dpf_WT_4

description:
RNA from single larva at mRNA
DreUjiNishi-334


title: 15dpf_WT_5

description:
RNA from single larva at mRNA
DreUjiNishi-335


title: 15dpf_WT_3

description:
RNA from single larva at mRNA
DreUjiNishi-333


title: KA808JBS-11

description:
Quantstudio 7K Flex
JSAUG1R01_137


title: 15dpf_WT_2

description:
RNA from single larva at mRNA
DreUjiNishi-332


title: 15dpf_WT_1

description:
RNA from single larva at mRNA
DreUjiNishi-331


title: DA807XHS-05

description:
Quantstudio 7K Flex
JSAUG1R01_136


title: EA80811P-10

description:
Quantstudio 7K Flex
JSAUG1R01_134


title: 12dpf_mut_9

description:
RNA from single larva at mRNA
DreUjiNishi-329


title: EA808FRW-03

description:
Quantstudio 7K Flex
JSAUG1R01_132


title: 12dpf_mut_10

description:
RNA from single larva at mRNA
DreUjiNishi-330


title: 12dpf_mut_7

description:
RNA from single larva at mRNA
DreUjiNishi-327


title: 12dpf_mut_8

description:
RNA from single larva at mRNA
DreUjiNishi-328


title: EA80894W-08

description:
Quantstudio 7K Flex
JSAUG1R01_131


title: CA8098CB-04

description:
Quantstudio 7K Flex
JSAUG1R01_133


title: 12dpf_mut_6

description:
RNA from single larva at mRNA
DreUjiNishi-326


title: GA808DDC-09

description:
Quantstudio 7K Flex
JSAUG1R01_129


title: FA807SVF-09

description:
Quantstudio 7K Flex
JSAUG1R01_128


title: DA80852H-10

description:
Quantstudio 7K Flex
JSAUG1R01_142


title: 15dpf_WT_6

description:
RNA from single larva at mRNA
DreUjiNishi-336


title: 12dpf_mut_4

description:
RNA from single larva at mRNA
DreUjiNishi-324


title: EA807ZRJ-01

description:
Quantstudio 7K Flex
JSAUG1R01_130


title: 12dpf_mut_5

description:
RNA from single larva at mRNA
DreUjiNishi-325


title: EA808LNC-12

description:
Quantstudio 7K Flex
JSAUG1R01_127


title: FA809Z40-08

description:
Quantstudio 7K Flex
JSAUG1R01_126


title: AA807Z6F-09

description:
Quantstudio 7K Flex
JSAUG1R01_125


title: 12dpf_mut_2

description:
RNA from single larva at mRNA
DreUjiNishi-322


title: KA80CTX0-02

description:
Quantstudio 7K Flex
JSAUG1R01_139


title: 12dpf_mut_3

description:
RNA from single larva at mRNA
DreUjiNishi-323


title: 12dpf_WT_6

description:
RNA from single larva at mRNA
DreUjiNishi-320


title: GA80B4GC-02

description:
Quantstudio 7K Flex
JSAUG1R01_123


title: 12dpf_mut_1

description:
RNA from single larva at mRNA
DreUjiNishi-321


title: 12dpf_WT_4

description:
RNA from single larva at mRNA
DreUjiNishi-318


title: BA808TCZ-09

description:
Quantstudio 7K Flex
JSAUG1R01_124


title: 12dpf_WT_3

description:
RNA from single larva at mRNA
DreUjiNishi-317


title: GA809BVW-10

description:
Quantstudio 7K Flex
JSAUG1R01_122


title: HA808GK1-08

description:
Quantstudio 7K Flex
JSAUG1R01_135


title: BA809C72-07

description:
Quantstudio 7K Flex
JSAUG1R01_121


title: 12dpf_WT_2

description:
RNA from single larva at mRNA
DreUjiNishi-316


title: AA809LF3-03

description:
Quantstudio 7K Flex
JSAUG1R01_120


title: 12dpf_WT_1

description:
RNA from single larva at mRNA
DreUjiNishi-315


title: JA807F5R-09

description:
Quantstudio 7K Flex
JSAUG1R01_119


title: 10dpf_mut_8

description:
RNA from single larva at mRNA
DreUjiNishi-314


title: JA808X6Z-08

description:
Quantstudio 7K Flex
JSAUG1R01_117


title: CA808WKC-04

description:
Quantstudio 7K Flex
JSAUG1R01_116


title: EA809SJN-08

description:
Quantstudio 7K Flex
JSAUG1R01_118


title: DA807H11-10

description:
Quantstudio 7K Flex
JSAUG1R01_115


title: 10dpf_mut_6

description:
RNA from single larva at mRNA
DreUjiNishi-312


title: 10dpf_mut_5

description:
RNA from single larva at mRNA
DreUjiNishi-311


title: AA808W7Y-15

description:
Quantstudio 7K Flex
JSAUG1R01_114


title: 10dpf_mut_7

description:
RNA from single larva at mRNA
DreUjiNishi-313


title: 10dpf_mut_3

description:
RNA from single larva at mRNA
DreUjiNishi-309


title: 10dpf_mut_4

description:
RNA from single larva at mRNA
DreUjiNishi-310


title: 10dpf_mut_2

description:
RNA from single larva at mRNA
DreUjiNishi-308


title: 10dpf_mut_1

description:
RNA from single larva at mRNA
DreUjiNishi-307


title: KA807L92-02

description:
Quantstudio 7K Flex
JSAUG1R01_112


title: CA80758F-02

description:
Quantstudio 7K Flex
JSAUG1R01_111


title: 10dpf_WT_6

description:
RNA from single larva at mRNA
DreUjiNishi-306


title: FA808RFZ-04

description:
Quantstudio 7K Flex
JSAUG1R01_109


title: JA809VT9-08

description:
Quantstudio 7K Flex
JSAUG1R01_107


title: FA80932R-12

description:
Quantstudio 7K Flex
JSAUG1R01_106


title: 10dpf_WT_2

description:
RNA from single larva at mRNA
DreUjiNishi-302


title: 10dpf_WT_5

description:
RNA from single larva at mRNA
DreUjiNishi-305


title: 10dpf_WT_1

description:
RNA from single larva at mRNA
DreUjiNishi-301


title: EA8082JF-09

description:
Quantstudio 7K Flex
JSAUG1R01_110


title: DA807837-07

description:
Quantstudio 7K Flex
JSAUG1R01_105


title: FA807H9Q-11

description:
Quantstudio 7K Flex
JSAUG1R01_108


title: 12dpf_WT_5

description:
RNA from single larva at mRNA
DreUjiNishi-319


title: FA809WTM-02

description:
Quantstudio 7K Flex
JSAUG1R01_103


title: CA8083JJ-11

description:
Quantstudio 7K Flex
JSAUG1R01_104


title: BA80BN7F-03

description:
Quantstudio 7K Flex
JSAUG1R01_102


title: 2d_5fu_rna

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

description:
Library name: 2d_5fu_rna
Targeted single-cell triomics analysis using the MissionBio tapestri platform

data_processing:
Data was processed using the Tapestri DNA + Protein v2.0.2 pipeline (MissionBio), modified to include the RNA data.
For DNA, data was processed using the Tapestri DNA + Protein v2.0.2 pipeline (MissionBio). Briefly, adapter trimming was performed using Cutadapt, reads greater than 30 bases were retained, and the barcode structures were extracted. The pipeline identified valid barcodes and barcodes that can be corrected for sequencing errors. Reads were mapped to the hg19 reference genome using the BWA-MEM algorithm. Cell calling was performed using a cut-off for total DNA reads where cells with a percent of DNA amplicons per barcode greater than 0.2X of the mean of all DNA amplicon reads were included. Variant calling in the DNA reads was performed using GATK. Cells were genotyped using the variant calls and cell lines identified from their known genotypes.
For RNA, adapter trimming was performed using Cutadapt, reads greater than 30 bases were retained, and the barcode structures were extracted. The pipeline identified valid barcodes and barcodes that can be corrected for sequencing errors. Reads were mapped to the hg19 reference genome using the STAR algorithm. Target reads that had more than five bases reading into the intron were removed.  RNA reads with cell barcodes corresponding to the cell barcodes identified as cells in the DNA library were used for downstream analysis.
For Proteins, data was processed using the Tapestri DNA + Protein v2.0.2 pipeline (MissionBio). Briefly, antibody barcodes were identified, including all variants with single base substitutions, to account for sequencing errors. Then, cell barcodes were extracted and added to the fastq header and adapters were trimmed. Using the error-corrected map for the antibody barcodes, the antibody barcodes were identified in the reads present in the trimmed fastq file. Subsequently, the capture sequence and PCR handle were also trimmed from the reads. If the remaining read sequence were of the desired length and matched any of the antibody barcodes in the error correction map, it was accepted. Then, the number of reads for each antibody barcode within a cell were counted to generate the final output file listing the cell barcodes and the number of antibody reads for each barcode.
Assembly: hg19
Supplementary files format and content: Triomics_data_processed.csv, processed and filtered data received from the MissionBio pipeline.

source_name: Breast; Mammary gland

growth_protocol: MCF7 cells (ATCC) were cultured in DMEM supplemented with 10 % fetal bovine serum, 1 % penicillin/streptomycin, 1% L-glutamine and 1 % non-essential amino acids . T-47D cells (ATCC) were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 1% sodium pyruvate and 1% L-glutamine. Cell culture conditions were 37°C and 5% CO2 in humidified atmosphere, and cells were not maintained for longer than 30 passages.

extract_protocol:
Cells from monolayer cultures were washed with PBS and detached with trypsin for 3 min, at 37°C. PDS slices were soaked 3 times in PBS and cells were detached with Corning Accutase for 5 min at 37 °C with gentle agitation at 180 rpm. Single-cell suspensions were then generated using a 25G needle and a 40 µm cell strainer. Dead cell removal was performed using the MACS Dead Cell Removal kit (Miltenyi), according to the manufacturer’s instructions.
The triomics experiment was performed using the Tapestri Single-Cell Multiomics V1.1 workflow (Mission Bio). Briefly, single-cell suspensions were stained using protein-targeting AOCs and subsequently diluted to ~3500 cells/ml. Stained cells were then encapsulated in droplets by the Tapestri instrument. Subsequently, cell lysis, reverse transcription and protease treatment was run. Custom panels for DNA and RNA was used and genomic DNA, cDNA and antibody tag sequences were barcoded in emulsion. Barcoding beads were cleaved off from targeted sequences using UV light. The target sequences were preamplified after which the emulsion was broken and libraries specific for DNA, RNA and protein targets were enriched and purified using Dynabeads MyOne Streptavidin and SPRI beads. Separate libraries for each analyte were then generated by PCR using Illumina primers. Final libraries were purified using SPRI beads before quantification and quality control using capillary gel-electrophoresis on a Fragment Analyzer. Libraries were pooled and sequenced according to the manufacturer’s instructions using 150 paired-end cycles, supplemented with 15% PhiX Control v3.

treatment_protocol: 5-fluorouracil was dissolved in saline solution. For treatment of monolayer cultures, 2 x 105 MCF7 cells and 3 x 105 T-47D cells were seeded in 6-well plates containing 2 ml of cell-specific media. After 24 hours, IC50 concentrations of 5-fluorouracil (100 µM for MCF7 and 200 µM for T-47D cells, respectively) was administrated for 48 hours. For treatment of PDS-cultured cells, 1 mM 5-fluorouracil was administrated for 48 hours.

value: Breast; Mammary gland

value: Mixed sample (MCF7, T47-D)

tag: culture

tag: library type

value: mRNA


title: 2d_5fu_dna

description:
Library name: 2d_5fu_dna
Targeted single-cell triomics analysis using the MissionBio tapestri platform

value: DNA


title: 2d_control_protein

description:
Library name: 2d_control_protein
Targeted single-cell triomics analysis using the MissionBio tapestri platform

library_source: other

molecule: protein

value: Control

value: ADT


title: FA8076J5-10

description:
Quantstudio 7K Flex
JSAUG1R01_100

value: Male


title: 2d_control_rna

description:
Library name: 2d_control_rna
Targeted single-cell triomics analysis using the MissionBio tapestri platform


title: JA8076MM-07

description:
Quantstudio 7K Flex
JSAUG1R01_113


title: 2d_5fu_protein

description:
Library name: 2d_5fu_protein
Targeted single-cell triomics analysis using the MissionBio tapestri platform


title: EA808SX3-08

description:
Quantstudio 7K Flex
JSAUG1R01_099


title: FA80BM0Y-08

description:
Quantstudio 7K Flex
JSAUG1R01_098

value: Alzheimer's Disease

value: Structure of nervous tissue


title: EA80741Q-11

description:
Quantstudio 7K Flex
JSAUG1R01_097


title: 2d_control_dna

description:
Library name: 2d_control_dna
Targeted single-cell triomics analysis using the MissionBio tapestri platform


title: dpi5_male

city: Thuwal

first: Laura

last: Sudupe

address: King Abdullah University of Science and Technology (KAUST)

country: Saudi Arabia

institute: KAUST

description: fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings.
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: spatial transcriptomics

organism: Mus musculus

source_name: Heart

extract_protocol:
The hearts from Collagen1α1-GFP 8-12 weeks old, healthy or infarcted mice (3 and 5 dpi) were excised and washed in PBS, embedded in OCT compound, frozen in dry ice and sectioned in a cryostat at a thickness of 10 μm at -20 °C following the manufacturer's recommendations. The RNA quality of the tissues was checked by extracting RNA from tissue sections with the Qiagen RNeasy extraction kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed with a 4200 TapeStation (Agilent Technologies), and all the samples had a RIN between 7.2 and 7.7. In the final experiment, the mRNA capture was performed following instructions of the Visium Spatial Gene Expression Reagent Kits User Guide (10x Genomics). For optimization of the tissue permeabilization, seven sections from the 3 dpi sample were collected onto a -20 °C pre-equilibrated Visium tissue optimization slide (10X Genomics) and the manufacturer’s recommendations were followed.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions.
Libraries were loaded at 650 pM and sequenced on a Nextseq 2000 System (Illumina) using a Nextseq2000 P3 Reagent Kit (100 cycles, Illumina), at an average sequencing depth of approximately 100,000 reads per spot (25-35% of the 5,000 total spots on the slide were used). Sequencing was performed using the following read protocol: Read1, 28 cycles; i7 index, 10 cycles; i5 index, 10 cycles; Read2, 91 cycles.

value: Heart

tag: genotype

value: male

value: myocardial infarction

tag: time point

value: 5 dpi


title: dpi3

value: female

tag: treatment

value: 3 dpi


title: 10dpf_WT_4

description:
RNA from single larva at mRNA
DreUjiNishi-304

value: whole organism

value: wild-type


title: 10dpf_WT_3

description:
RNA from single larva at mRNA
DreUjiNishi-303


title: dpi5_female


title: AA807X29-07

description:
Quantstudio 7K Flex
JSAUG1R01_101

tag: donor id

value: Healthy Control

value: Circulating blood

value: Venous

value: Plasma

value: total cell-free biofluid RNA


title: EA80D20Q-08

description:
Quantstudio 7K Flex
JSAUG1R01_096

tag: subject status

value: Lumbar Puncture

value: Cerebral Spinal Fluid


title: CA8099TM-03

description:
Quantstudio 7K Flex
JSAUG1R01_095

value: Alzheimer's Disease

tag: Sex

value: Male


title: control

value: Heart

value: control


title: JA809R0Q-08

description:
Quantstudio 7K Flex
JSAUG1R01_091

tag: age

value: Structure of nervous tissue


title: HA80C6GF-02

description:
Quantstudio 7K Flex
JSAUG1R01_088

tag: anatomical location


title: AA807P5C-07

description:
Quantstudio 7K Flex
JSAUG1R01_090

tag: sample collection method


title: FA807N6L-03

description:
Quantstudio 7K Flex
JSAUG1R01_087

tag: starting amount


title: JA80818H-09

description:
Quantstudio 7K Flex
JSAUG1R01_089

value: Female

tag: holding temperature


title: JA8088XM-08

description:
Quantstudio 7K Flex
JSAUG1R01_086

tag: molecule type


title: Spheroid Day 14 - D

city: Atlanta

first: Alejandro

last: de Janon

state: GA

address: 225 North Ave NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

description: Library name: Sample 20

data_processing:
Alignment was performed using STAR Alignment software V 2.7.11b
Raw FASTQ files were analyzed for quality using FastQC and summarized with MultiQC to assess sequencing quality metrics. Reads were aligned to the human reference genome (GRCh38) using STAR aligner (version 2.7.11b) with default parameters.
Assembly: GRCh38.p13
Supplementary files format and content: comma-separated values

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: Cells cultured in Vascular Cellular Basal Media supplemented with 5 ng/ml VEGF, 5 ng/ml EGF, 5 ng/ml FEF, 15 ng/ml IGF-1, 10 mM L-glutamine, 0.75 U/ml heparin sulfate, 1 µg/ml hydrocortisone, and 50 µg/ml ascorbic acid

extract_protocol:
Pooled organoid were washed in PBS and lysed in RLT buffer with 1% beta-mercaptoethanol.
Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and integrity were assessed using both the Agilent Bioanalyzer and NanoDrop spectrophotometer. Only high-quality RNA samples were used for library preparation. RNA-seq libraries were prepared using the P3 XLEAP 200-cycle kit, targeting a sequencing depth of approximately 1.2 billion reads per run. Libraries were quantified, pooled, and sequenced on the Illumina NextSeq 2000 platform to generate paired-end reads.

tag: cell type

value: Bone Marrow Mesenchymal Stem Cell

value: Human Umbilical Vein Endothelial Cells

value: 14 days culture time no Matrigel


title: DA808BTB-09

description:
Quantstudio 7K Flex
JSAUG1R01_084

tag: tissue


title: EA807W1W-08

description:
Quantstudio 7K Flex
JSAUG1R01_085


title: Spheroid Day 14 - A

description: Library name: Sample 17


title: Spheroid Day 14 - C

description: Library name: Sample 19


title: KA808P5Z-04

description:
Quantstudio 7K Flex
JSAUG1R01_083


title: Organoid Day 60 - D

description: Library name: Sample 16

value: 60 days culture time with Matrigel


title: HA80BCF3-08

description:
Quantstudio 7K Flex
JSAUG1R01_082


title: Spheroid Day 14 - B

description: Library name: Sample 18


title: Organoid Day 60 - C

description: Library name: Sample 15


title: GA8083DJ-13

description:
Quantstudio 7K Flex
JSAUG1R01_092

value: Healthy Control


title: FA80805Z-06

description:
Quantstudio 7K Flex
JSAUG1R01_093

value: Circulating blood


title: WT_no_N_rep2

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

description: Gene expression after cultivation for 48 h in BG11-N medium without any source of nitrogen

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Here, the raw data are submitted. For further analysis, raw data were normexp background corrected (Ritchie et al., 2014) and quantile normalized using the limma R package (Ritchie et al., 2007). The transcriptome differences were calculated between WT and ∆sniP3 deletoin mutant for the two different conditions with or without nitrogen.

organism: Synechocystis sp. PCC 6803

source_name: liquid culture

label_protocol: 5 µg total RNA was DNase-treated. Then, DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. For hybridization to microarrays, 600 ng of the labeled RNA was used. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: The Synechocystis 6803 substrain M (Trautmann et al., 2012) was used throughout. The generation of the ∆sniP3 mutant was described in detail by Alvarenga-Lucius et al. (2025). The wild-type (WT) and ∆sniP3 mutant strains were grown in glass Erlenmeyer flasks (250 mL) filled with 100 mL of BG11 buffered medium (pH 8.0) without sodium carbonate (Rippka et al., 1979) under the following conditions: 28 ± 2°C, continuous light of 50 μmol photons m-2 s-1 with continuous shaking at 130 rpm (standard growth conditions). Growth experiments were performed for 48 h under continuous light of 100 μmol photons m-2 s-1 in BG11 medium with nitrogen, or without. The ∆sniP3 mutant was grown in the presence of 50 µg mL-1 kanamycin during pre-culture and without antibiotics during the experiments for accurate comparison with the WT.

extract_protocol: Aliquots of 10 mL were collected by centrifugation at 7,000 g for 5 min at 4°C and the pellet was frozen in liquid nitrogen. Total RNA was prepared using the PGTX method (Pinto et al., 2009).

treatment_protocol: Gene expression analyses were performed after shifts to 100 μmol photons m-2 s-1 for 48 h in the presence (BG11 medium) or absence of any source of nitrogen (BG11-N medium). The cultures were precultivated under continuous light of 50 μmol photons m-2 s-1 (standard growth conditions).

tag: strain

value: PCC-M

value: wild type


title: WT_no_N_rep1


title: dsniP3_with_N_rep1

description: Gene expression in BG11 medium with nitrogen under standard growth conditions

value: deltasniP3 mutant


title: dsniP3_with_N_rep2


title: dsniP3_no_N_rep2


title: WT_with_N_rep1


title: JA808GXS-09

description:
Quantstudio 7K Flex
JSAUG1R01_080

value: Lumbar Puncture

value: total cell-free biofluid RNA


title: Organoid Day 60 - B

description: Library name: Sample 14


title: EA808CZ4-09

description:
Quantstudio 7K Flex
JSAUG1R01_079

value: Cerebral Spinal Fluid


title: GA807QK3-10

description:
Quantstudio 7K Flex
JSAUG1R01_094

value: Male


title: BA80B8NT-04

description:
Quantstudio 7K Flex
JSAUG1R01_078

value: Venous

value: Plasma


title: KA80896J-02

description:
Quantstudio 7K Flex
JSAUG1R01_077

value: Alzheimer's Disease


title: Organoid Day 28 - D

description: Library name: Sample 12

value: 28 days culture time with Matrigel


title: Organoid Day 28 - C

description: Library name: Sample 11

value: Bone Marrow Mesenchymal Stem Cell


title: GA80B3MJ-13

description:
Quantstudio 7K Flex
JSAUG1R01_074

value: Structure of nervous tissue


title: FA809RBR-08

description:
Quantstudio 7K Flex
JSAUG1R01_076

value: Female


title: Organoid Day 14 - D

description: Library name: Sample 8

value: Human Umbilical Vein Endothelial Cells

value: 14 days culture time with Matrigel


title: dsniP3_no_N_rep1


title: Organoid Day 28 - A

description: Library name: Sample 9


title: Organoid Day 28 - B

description: Library name: Sample 10


title: GA80BHF1-02

description:
Quantstudio 7K Flex
JSAUG1R01_075

value: Circulating blood


title: KA809DS9-02

description:
Quantstudio 7K Flex
JSAUG1R01_073

value: Healthy Control


title: WT_with_N_rep2

value: PCC-M

value: wild type


title: Organoid Day 14 - C

description: Library name: Sample 7


title: Organoid Day 14 - B

description: Library name: Sample 6


title: CA808370-08

description:
Quantstudio 7K Flex
JSAUG1R01_072

value: Lumbar Puncture


title: AA80BDD1-09

description:
Quantstudio 7K Flex
JSAUG1R01_071

value: total cell-free biofluid RNA


title: AA8086VQ-03

description:
Quantstudio 7K Flex
JSAUG1R01_081


title: Organoid Day 14 - A

description: Library name: Sample 5


title: Organoid Day 60 - A

description: Library name: Sample 13

value: 60 days culture time with Matrigel


title: Organoid Day 3 - D

description: Library name: Sample 4

value: 3 days culture time with Matrigel


title: DA808ZL5-12

description:
Quantstudio 7K Flex
JSAUG1R01_067

value: Male

value: Cerebral Spinal Fluid


title: BA8088QD-09

description:
Quantstudio 7K Flex
JSAUG1R01_069


title: EA808PNQ-11

description:
Quantstudio 7K Flex
JSAUG1R01_070

value: Venous

value: Plasma


title: Organoid Day 3 - C

description: Library name: Sample 3

value: Bone Marrow Mesenchymal Stem Cell


title: Mnase-seq rep2

city: Dortmund

first: Max

last: Haase

address: Otto-Hahn-Str. 11

institute: Max Planck Institute of Molecular Physiology

description: Library name: H_uvarum_MNase1U

data_processing:
Data was processed first by removal of sequencing adaptors with Trimmomatic (v0.39). Then reads were aligned to the H. uvarum HuvaT2T genome build using the Burrows Wheeler aligner (BWA) mem algorithm (v0.7.7). Cse4-enriched regions were determined by taking the ratio of reads mapping from the tagged sample (Cse4-mNeonGreen) to the input control (WT, untagged). Further, Cse4-mNG nucleosome dyads were determined using the deeptools program (v3.5.2).
Assembly: HuvaT2T
Supplementary files format and content: Each process file is provided as a BigWig file

organism: Hanseniaspora uvarum

growth_protocol: Cells of H. uvarum were grown in YPD at 30˚C until reaching mid-log phase

extract_protocol:
DNA to be sequenced were extracted by digestion of crosslinked chromatin by MNase and Cse4-bound DNA was eneriched by IP of Cse4 using a mNeonGreen Nanobody.
Libraries were made using the NEBNext® Ultra™ II Illumina kit

treatment_protocol: Cells were cross-linked prior to DNA extraction

tag: cell line


title: BA807NGQ-11

description:
Quantstudio 7K Flex
JSAUG1R01_066


title: DA80BHJ6-02

description:
Quantstudio 7K Flex
JSAUG1R01_068

value: Alzheimer's Disease


title: Organoid Day 3 - A

description: Library name: Sample 1


title: Organoid Day 3 - B

description: Library name: Sample 2


title: Mnase-seq rep1

description: Library name: H_uvarum_MNase10U


title: EA80JJRL-01

description:
Quantstudio 7K Flex
JSAUG1R01_064

value: Female


title: JA8080XH-03

description:
Quantstudio 7K Flex
JSAUG1R01_061


title: HA8082LZ-12

description:
Quantstudio 7K Flex
JSAUG1R01_062

value: Structure of nervous tissue


title: JA807FS6-09

description:
Quantstudio 7K Flex
JSAUG1R01_063


title: CA8071QS-11

description:
Quantstudio 7K Flex
JSAUG1R01_065


title: Th1/17 cells, Control cohort, Biol rep 12

city: Kingston

first: Chandrakant

last: Tayade

address: 18 Stuart Street

institute: Queen's University

description: Library name: EDCV045_Th1-17_S6

data_processing:
Reads were trimmed to remove adaptor sequences and low-quality bases using Trimmomatic. Trimmed reads were aligned to the human reference genome (GENCODE/GRCh38) using STAR. Gene-level read counts were generated using HTSeq. The resulting raw counts for each sample are provided in the matrix (tsv file).
Assembly: Homo_sapiens:GRCh38
Supplementary files format and content: tsv file includes raw counts for each Sample

source_name: Peripheral Blood/PBMCs

growth_protocol: Prior to sorting cells (FACS), PBMCs were briefly thawed in a water bath at 37C. Cell suspensions were added to warm RPMI media with 10% FBS and centrifuged at 400RCF for 10mins at 20C prior to resuspending in 2% FACS buffer and counting cells. CD4+ T cells were then isolated using a commercially available kit (17952, StemCell, Canada), as per manufacturer’s protocol. CD4+ T cells were washed and resuspended in warm TexMACS media (130-097-196, Miltenyi Biotec, USA) prior to seeding in 96-well plates at 1x10^6 cells/well.

extract_protocol:
RNA was isolated using RNeasy Micro Kit (74004, Qiagen, Canada), as per manufacturer’s guidelines. RNA purity was assessed using the Nanodrop Spectrophotometer (ThermoFisher, Canada) prior to storage at -80C.
Total RNA purity was assessed prior to library preparation. RNA samples were processed at the McGill Genome Centre (Quebec, Canada) using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) with poly (A) mRNA enrichment. Libraries were generated according to standard NEBNext protocols including mRNA capture, fragmentation, first- and second-strand cDNA synthesis, end repair, adaptor ligation, and PCR amplification. Libraries underwent Ampure XP bead clean-up and quality assessment (LibQC), including removal of primer dimer fragments, before pooling and sequencing on an Illumina NovaSeq X Plus platform using paired-end reads.

treatment_protocol: Cells were re-stimulated prior to FACS staining using 30ng/mL of PMA and 1ug/mL of ionomycin and incubated for 4h at 37C with 5% CO2. Following incubation, IFNg-secreting and IL-17-secreting cells were fluorescently labelled using IFNg Secretion Assay – Detection Kit (FITC; 130-090-433, Miltenyi Biotec, Canada) and IL-17 Secretion Assay – Detection Kit (PE; 130-094-537, Miltenyi Biotec, Canada), as per manufacturer’s protocol. This was conducted to avoid permeabilizing cells to allow for downstream analysis. During staining, cells were also labelled with CD3 (300312) and CD4 (300511) extracellular Abs, as well as the viability dye (423102), all products were purchased from BioLegend unless otherwise stated. Following washing, cells were resuspended in 2% FACS buffer for FACS sorting. Cells were sorted into viable populations of Th17 (CD3+CD4+IFNg-IL-17+), Th1/17 (CD3+CD4+IFNg+IL-17+), and Th1 cells (CD3+CD4+IFNg+IL-17-) in collection media, consisting of 50% FBS and 50% phenol-free RPMI 1640 medium (11835030, ThermoFisher, Canada). Samples were stored on ice, added to respective DNA LoBind Tubes (EP022431021, Millipore Sigma, Canada), and centrifuged at 400RCF for 10mins at 4C before resuspending pellets in 300uL of RNAprotect Cell Reagent (76526, Qiagen, Canada). Cells were stored at -80C prior to RNA isolation.

value: Peripheral Blood/PBMCs

value: Primary CD4+ T cells

value: Th1/17 Cells

tag: rasrm disease_stage_(1-4)

value: Control

tag: race

value: Caucasian

tag: bmi

tag: education

value: Post secondary


title: GA8090T6-03

description:
Quantstudio 7K Flex
JSAUG1R01_059

tag: donor id

value: Circulating blood

value: total cell-free biofluid RNA