title: duodenum organoids, grown in OGM, 7 days, rep 3

city: South San Francisco

first: Julia

last: Co

address: 1 DNA Way

institute: Genentech

data_processing:
Base-calling and quality control were performed by Novogene, Inc.
Gene mapping was performed by Novogene, Inc.
Assembly: GRCh38/hg38
Supplementary files format and content: gene_fpkm.txt is a tab-delimited file containing gene counts in FPKM for all genes in reference genome for all conditions. The gene_id header refers to the Ensembl gene ID. The sample name headerss refer to the readcounts for that sample. The gene_name header refers to the gene symbol. The gene_chr header refers to the chromosome/scaffold ID. The gene_start header refers to the chromosomal start coordinate, and gene_end refers to the end coordinate. The gene_strand header refers to the strand specificity of the gene. The gene_length header provides the gene length in bp. The gene_biotype header provides the gene type. The gene_description header provides a description from PFAM Annotation. The tf_family header provides the TF family for the gene if applicable.

source_name: duodenum

growth_protocol: Duodenum organoids grown in adherent BME culture with growth media (Intesticult OGM, STEMCELL Technologies) or differentiation media (Intesticult ODM STEMCELL technologies)

extract_protocol:
RNA was harvested and stored in RLT plus buffer (Qiagen) and extracted by Novogene Inc. At least 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

treatment_protocol: Proliferative organoids grown for 7 days in OGM. Differentiated organoids grown in OGM 7 days then transferred to ODM for 4 days.

value: duodenum

value: intestinal epithelial cells

value: WT

value: d7 OGM


title: Mutant_S6, 7DPI, rep1

status: Public on Jan 23 2025

type: SRA

city: Fargo

first: Lili

last: Qi

state: ND

address: 1616 Albrecht Blvd. North

country: USA

institute: USDA-ARS

library_source: transcriptomic

data_processing:
Adapters were trimmed and low-quality reads were discarded using Trimmomatic version 0.38
Mapping of apadter trimmed RNA-Seq reads to the sunflower XRQr2.1 reference genome assembly was performed using HISAT2
Transcript assembly and quantification was performed using StringTie (Pertea et al., 2016) and count data was extracted using the Python script prepDE.py3 (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py3).
Differentially expressed genes for comparisons across timepoints and between HA-R9 and mutant lines were subsequently identified using DESeq2
Assembly: XRQr2.1
Supplementary files format and content: File R11_gene_count_matrix.txt is a tab-delimited text file containing read count data for all 27 RNA-seq samples

molecule: total RNA

organism: Helianthus annuus

source_name: Leaf

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared by The Genewiz corporation, NJ, USA following their protocols.

tag: tissue

value: Leaf

tag: genotype

tag: treatment

value: Rust inoculation

tag: time

value: Day 7


title: duodenum organoids, differentiated in ODM, 4 days, rep 2

state: California

organism: Homo sapiens

tag: cell line

tag: cell type

value: d4 ODM


title: Mutant_S6, 0DPI, rep2

value: Day 0


title: Epidermis, WT, rep 2

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Raw FASTQ reads were quality trimmed using fastp (version 0.23.2 length cutoff 20, quality cutoff 15). Adapter trimming was disabled due to the presence of BD Rhapsody multiplexing sequences.
The UMI, complex barcode, and sample tags were extracted and demultiplexed using custom scripts. Demultiplexed samples can be found in Supplementary Files.
Reads were mapped to the mouse reference genome version GRCm39, with Gencode annotations vM29, filtered for protein-coding genes and lncRNAs, using STAR version 2.7.10a (--soloType Droplet –soloCellFilter None –soloFeatures GeneFull_Ex50pAS –soloCBstart 1 –soloCBlen 27 –soloUMIstart 28 –soloUMIlen 8–soloCBwhitelist rhapsody_whitelist.txt –soloMultiMappers EM).
Raw counts were imported as AnnData objects. We removed low complexity barcodes with the knee plot method (<1200 counts per cell), and further filtered out cells with a high mitochondrial mRNA percentage (>20%). Doublets were predicted with scrublet. Finally, each sample’s gene expression matrix was normalized using scran (1.22.1) with Leiden clustering input at resolution 0.5.
At this stage samples were merged with scanpy (1.9.1). For 2D embedding, the expression matrix was subset to the 3,000 most highly variable genes (sc.pp.highly_variable_genes, flavor “seurat”). The top 100 principal components (PCs) were calculated, and batch-corrected using Harmony (0.0.5). The PCs served as basis for k-nearest neighbor calculation (sc.pp.neighbors, n_neighbors=30), which were used as input for UMAP layout (sc.tl.umap, min_dist=0.3). Leiden clustering at resolution 0.8 was used to annotate cell clusters based on known marker genes.
Assembly: mm39
Supplementary files format and content: Tab-separated values, MatrixMarket matrix files
Supplementary files format and content: AnnData file

organism: Mus musculus

source_name: Epidermis

extract_protocol:
Back skin of. control and Cers4 epi -/-  P19 female mice were dissected and single cell suspensions were generated using a mixture of DNAse I (40 µg/ml), Liberase (0.125mg/ml; Roche Cat.NO. 05401119001 and Papain (30 U/ml Worthington Cat. NO. LK003150) digestion in S-MEM (Gibco) for 60 min at 37 °C.
Cells were labeled with Mouse Immune Single-Cell Multiplexing Kit (BD) according to manufacturers instructions. Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD, 633802) and sequenced on the Illumina NextSeq 500 using High Output Kit v2.5 (150 cycles, Illumina) for 2 × 75 bp paired-end reads with 8 bp single index aiming at sequencing depth of >20,000 reads per cell for each sample.

value: Epidermis

tag: strain


title: duodenum organoids, differentiated in ODM, 4 days, rep 3


title: Liver_5um_4

city: Wuhan

first: Xuan

last: Niu

state: --- Select One ---

address: 238, Jiefang road

country: China

institute: Wuhan university

data_processing:
Differentially expressed genes (DEGs) between the H2O and MPs groups were analyzed using linear models for the microarray data (limma) package in R.
The heatmap was drawn by the R package pheatmap.
The shared DEGs between each MPs group and the H2O group were identified by drawing a Venn diagram.
Gene ontology (GO, http://www.geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.kegg.jp/) pathway enrichment analyses of DEGs were performed by using DAVID online tools (https://david.ncifcrf.gov/).
The protein‒protein interaction (PPI) network was predicted using the STRING database (http://string-db.org, version 11.5)
Assembly: NCBI (GCF_000001635.26_GRCm38.p6)
Supplementary files format and content: tab-delimited text file includes raw expression of genes for each sample
Supplementary files format and content: tab-delimited text file includes raw expression of RNA for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the livers of mice using RNA isolation kit (#R6934–01, Omega Bio-Tek, USA) according to the manufacturer's instructions
TOYOBO ReverTra Ace qPCR RT kit was utilized for reverse transcription

value: Liver

value: ICR

tag: Sex

value: Male


title: duodenum organoids, differentiated in ODM, 4 days, rep 1


title: Epidermis, Cers4epi-/-, rep 2

description: BD Rhapsody


title: duodenum organoids, grown in OGM, 7 days, rep 2


title: ALPHA-mouse-IL4-cd22-4A

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: TRA chain

library_source: other

data_processing:
10X Genomics: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Hashtags 10X Genomics: Processing of the HTO samples was performed using CITEseq-Count,
Bulk RNAseq: Basecalling performed using Illumina bcl2fastq v2.20 Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence Reads were processed for mapping and quantification using nf-core rnaseq pipeline v3.0.0 (https://nf-co.re/rnaseq/3.0/usage ) and using Gene set from Ensembl.org release 102.
BD Rhapsody : Data were processed using rhapsody_wta_2.0b2 pipeline ( https://bitbucket.org/CRSwDev/cwl/src/master/v2.0b2/ ) from BD Genomics.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-seq

molecule: other

source_name: spleen

extract_protocol:
scRNA-seq: spleen or mesLN tissue were harvested and cells were dissociated  using PBS, scissors and syringe plunger on a 40um cell strainer. After washing, cells were counted and CD8+ T cells were enriched using negative selection Mojo Sort magnetic beads (Biolegend). mesLN cells were further stained to detect CD124+ and CD124- CD8+ T cells (anti-CD124-BV421, anti-CD8-FITC, anti-CD44-PECy7, anti-TCRb-BV711, DAPI),  cells and sorted using a FACS Aria uIII (BD Biosciences). Then cells were tagged using mouse multiplexing HashTags 1 to 6 (TotalSeq, Biolegend) or using Mouse multiplexing Sample Tag 1 and 2 (BD Biosciences) before pooled were made. Cell capture was performed using 10X Genomics Chromium controller (spleen samples) or using the BD Rhapsody scanner and express (mesLN).
RNA-seq and TCR-seq: spleens  were harvested and cells were dissociated using PBS, scissors and syringe plunger on a 40um cell strainer. After washing, cells were counted and CD8+ T cells were enriched using negative selection Mojo Sort magnetic beads (Biolegend). Enriched CD8+ T cells were further stained using (anti-CXCR3-BV421, anti-CD8-FITC, anti-CD44-PECy7, anti-TCRb-BV711, anti-CD49d-BV650, anti-CD22-PE, DAPI) and subpopulations sorted using a FACS Aria uIII (BD Biosciences) for each individual mouse (200,000 cells per mouse). Then, total RNA was extracted using the RNeasy micro kit (Qiagen) and eluted in 14 uL of distilled RNAse-free water before stored at -80°C for less then 2 weeks. RNA integrity was analysed using a 2100 Bioanalyzer (Agilent).
scRNA-seq: Chromium Single Cell 3’ v3 chemistry (10X Genomics) or BD Rhapsody Whole Transcriptome Analysis cDNA synthesis (BD Biosciences)
RNA-seq: SMART-seq HT cDNA synthesis kit (Takara)
TCR-seq: template-switch anchored RT-PCR using oligodT during the cDNA generation and the following mouse-specific Cα and Cβ primers for the PCR amplification: TRAC ‘5-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTCCTGAGACCGAGGATCTTT and TRBC ‘5-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGGTAGCCTTTTGTTTGTTTG (adapters in italic)

treatment_protocol: IL-4c treatment consisted in the administration of combined recombinant mouse IL-4 (5ug, Biolegend) with monoclonal anti-IL-4 antibody (11B11 clone, 25ug, Biolegend) at day -4 and at day -2 intrapertioneally in 100 uL sterile PBS. H. polygyrus infection consisted in the administration by oral gavage of 200 uL distilled water containing 200 infectious L3 larvae.

value: spleen

value: IL4c treated CD22+ Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: Liver_5um_2


title: Mutant_S6, 0DPI, rep1


title: Epidermis, Cers4epi-/-, rep 1

description: BD Rhapsody


title: Liver_5um_3


title: duodenum organoids, grown in OGM, 7 days, rep 1

value: duodenum


title: Epidermis, WT, rep 1

description: BD Rhapsody


title: WT, 14DPI, rep3

value: Day 14


title: Liver_5um_1

value: WT


title: GBM049

city: Baltimore

first: Srinivasan

last: Yegnasubramanian

address: 1650 Orleans Street

institute: Johns Hopkins University

description: FFPE 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 GRCh38 genome to gene expression count using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count matrix
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg: image of tissue alignment
Supplementary files format and content: cytassist_image.tiff: tissue image captured by CytAssist
Supplementary files format and content: spatial_enrichment.csv: list of spatial barcodes and gene expression
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
FFPE tissue block was placed in a microtome, and 5um sections were cut for blank slides
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium CytAssist Spatial Gene Expression Reagent Kits according to manufacture's construction
CytAssist spatial transcriptomics

value: Brain


title: XXX, Input, rep2

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

data_processing:
Trim Galore was used to filter the raw data.
Clean reads were aligned to the Drosophila reference genome using HISAT2.
exomePeak2 was used for m6A peak calling.
The common m6A peaks were obtained by intersection of two biological replicates.
Assembly: Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa
Supplementary files format and content: bed files of m6A peaks.
Library strategy: MeRIP-Seq

organism: Drosophila melanogaster

source_name: third-instar larvae

growth_protocol: All the stocks are incubated at 25 degree.

extract_protocol:
Immunoprecipitation of m6A RNA was performed using GenSeq® m6A RNA IP kit. The NEBNext® Ultra II Directional RNA Library Prep kit was used for RNA sequencing library construction.
The sequencing library was constructed by removing ribosomal RNA.

value: third-instar larvae

value: metafemale

value: female

tag: antibody


title: WT, 14DPI, rep2

value: Leaf

value: Rust inoculation


title: XXX, IP, rep2


title: Liver_0.5um_4


title: GBM030

description: FFPE spatial transcriptome sequencing


title: XXX, Input, rep1


title: Liver_0.5um_3


title: WT, 14DPI, rep1


title: WT, 7DPI, rep3

value: Day 7


title: PICS3

city: Shanghai

first: Xingfeng

address: Shenyang Road 128#, Yangpu District

institute: Obstetrics and Gynecology Hospital of Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.  Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Blood

extract_protocol:
Whole blood was diluted with 1× PBS (1:1), layered on top of Ficoll-Paque Plus (Cytiva, USA), and centrifuged at 400 g for 30 min. The PBMC layer was isolated and washed twice with Dulbecco's phosphate buffered saline (DPBS) at 300 g for 10 min, followed by the removal of erythrocytes with red blood cell lysate on ice. After centrifugation, the cells were resuspended in RPMI1640 containing 10% fetal bovine serum (FBS). Cell viability was verified using trypan blue and approached 90% for each sample. Cells with high viability were subjected to library preparation.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: Blood samples were processed as follows. Anticoagulant was mixed upside down prior to use. The anticoagulant blood volume was accurately measured and equal volume of PBS was added. The centrifugal tube was placed flat and slowly rotated to evenly mix the PBS and blood. A lymphocyte separator equal to the volume of the mixture was added to another centrifuge tube. The centrifuge tube of the lymphocyte separator was tilted to an angle of 30-45 degrees on the horizontal plane. Liquid from the mixture tube was slowly poured into the lymphocyte separation tube along the wall. When the anticoagulant blood covered the liquid surface of the separation solution, the dumping was slightly accelerated, and the separation tube was slowly returned to a vertical position. After the blood was completely poured into the separation tube, the separation solution and the blood were stratified. Using a centrifugal tube to minimize vibration, samples were centrifuged at 800 g for 20 min. A pipette was directly inserted into the middle layer and the lymphocytes along the tube wall were slowly extracted and transferred into a new 1.5 mL centrifuge tube. The samples were centrifuged at 2000 rpm for 10 min. Finally, the liquid was slowly collected from the centrifuge tube with 200 µL pipette while avoiding the cell precipitate.The pelleted cells were resuspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% bovine serum albumin (BSA), the cell pellets were resuspended in PBS containing 0.04% BSA and re-filtered through a 35-μm cell strainer. Single cells were stained with acridine orange (AO)/ propidium iodide (PI) for viability assessment using a Countstar fluorescence cell analyzer.

value: Blood

value: peripheral blood mononuclear cells

tag: disease state

value: PICS-alive


title: Liver_0.5um_1

value: Liver

value: ICR

value: Male


title: Liver_0.5um_2


title: Liver_80nm_4


title: XXX, IP, rep1


title: HC5

value: HC


title: WT, 7DPI, rep2


title: Sepsis3

value: sepsis


title: HC3


title: WT, 7DPI, rep1


title: 2LM, Input, rep2

value: trisomy 2L

value: male


title: 2LM, IP, rep2


title: WT, 0DPI, rep3

value: WT

value: Day 0


title: Liver_80nm_3


title: 2LM, Input, rep1

value: third-instar larvae


title: Sepsis2


title: WT, 0DPI, rep2


title: Liver_80nm_2


title: Sepsis4


title: 2LM, IP, rep1


title: WT, 0DPI, rep1


title: PICS5


title: Liver_80nm_1


title: 2LF, Input, rep2

value: female


title: Tomato MF20 rep3

city: 云南省

first: 郭

last: 雅妍

address: 云南省昆明市盘龙区沣源路452号云南农业大学

department: 园林园艺学院

institute: 云南农业大学

description: Library name: MF20_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: AEKE03
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: fruits

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: fruits

tag: developmental stage

value: 55 days after flowering

tag: species no.


title: LOUCY, input

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

description: LOUCY, input

library_source: genomic

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to using BWA 0.7.17.
Read duplicates were removed using Picard 2.22.3 and multimapping reads were also removed.
Coverage/signal files (bigWig) were produced using DeepTools 3.4.3 bamCoverage.
Assembly: hg19
Supplementary files format and content: ChIP-Seq: Data were filtered to remove PCR duplicates and reads mapping to >2 genomic sites. Then bigwig display files were generated with deepTools bamCoverage and UCSC wigToBigWig.

molecule: genomic DNA

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 20% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Cells were crosslinked by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS.  Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples (vehicle-treated only), 1:8 diluted sonicated chromatin (whole cell extract) was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced  on the Illumina NovaSeq 6000 (151 bp reads) .

value: T-cell acute lymphoblastic leukemia

value: LOUCY

tag: chip-seq antibody


title: Liver_H2O_4


title: Tomato MF20 rep2

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: MF20_2


title: 2LF, IP, rep2


title: LOUCY, ZMIZ1

description: LOUCY, ZMIZ1


title: 2LF, Input, rep1


title: Tomato MF19 rep3

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: MF19_3


title: Tomato MF19 rep2

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: MF19_2


title: HC-03

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

value: Blood

value: peripheral blood mononuclear cells


title: MASH liver 4

city: Los Angeles

first: Bishuang

last: Cai

state: CA

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
A tab-delimited matrix file containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: liver

extract_protocol:
Total liver RNA from mice was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions
RNA-seq library construction was performed at BGI with a standard polyA-enrichment protocol.

value: liver

tag: age

value: 18 weeks

value: MASH diet


title: Liver_H2O_2

value: Liver

value: ICR

value: Male


title: HC-02

value: HC


title: Liver_H2O_1

value: WT


title: Tomato MF19 rep1

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: MF19_1


title: MASH liver 3


title: WTM, IP, rep2

value: wild type

value: male


title: WTM, Input, rep1

value: third-instar larvae


title: Tomato MF20 rep1

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: MF20_1

value: fruits


title: Tomato Br20 rep3

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: Br20_3

value: 40 days after flowering


title: AS-02

value: Sepsis


title: MASH liver 2


title: HC-01


title: WTM, IP, rep1


title: Tomato Br20 rep2

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: Br20_2


title: AS-01


title: Liver_H2O_3


title: MASH liver 1


title: 2LF, IP, rep1

value: trisomy 2L

value: female


title: WTF, Input, rep2


title: Tomato Br20 rep1

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: Br20_1


title: WTF, IP, rep2


title: WTM, Input, rep2


title: PA-01

value: Blood

value: peripheral blood mononuclear cells

value: PICS-alive


title: WTF, Input, rep1


title: Tomato Br19 rep2

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: Br19_2


title: Chow liver 3

value: liver

value: 18 weeks

value: Chow diet


title: Chow liver 2

value: Male


title: PD-01

value: PICS-death


title: WT3_control

status: Public on Jan 22 2025

city: Gainesville

first: Robert

middle: John

last: Cousins

state: FL

address: 572 Newell Drive

department: Food Science/Nutrition

institute: University of Florida

data_processing:
CLC Genomics Workbench v 11.0.1
University of Florida NextGen DNA Sequencing Core Facility. The resulting FastQ files were downloaded to the University of Florida HiPerGator computing cluster.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized data

source_name: Intestine, duodenum

extract_protocol:
Intestinal epithelial cells were isolated as above and were further purified for flow cytometry and cell sorting (5). The preserved IECs were sent to MedGenome, Foster City, CA, USA).
Nuclei were isolated from the IECs and incubated with pre-loaded Tn5 transposase (Cat # FC-121-1030, Illumina, CA, USA) and sequencing adapters. The assembled protein A-Tn5 adapter transposome was activated by Mg2+ to generate adapter-flanked DNA fragments cut near the proteins of interest. The transposed DNA was then extracted, and PCR amplified using NEBNext High-Fidelity PCR Master Mix (Cat # M0541S, New England Biolabs, MA, USA). The library was purified with AMPure XP Magnetic Beads (Cat # A63880, Beckman Coulter, CA, USA), and its quality was assessed using a BioAnalyzer High-Sensitivity DNA Analysis kit (Cat # 5067–4626, Agilent, CA, USA).

value: Intestine, duodenum

value: IEC

value: Intestinal epithelial cells (IECs)

value: WT


title: KO9_global KO

value: KO


title: WT2_control


title: WT1_control


title: KO8_global KO


title: Tomato Br19 rep3

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: Br19_3

value: fruits

value: 40 days after flowering


title: WT5_control


title: WTF, IP, rep1

value: third-instar larvae

value: wild type


title: PD-02

value: Blood


title: KO7_global KO


title: Tomato Br19 rep1

address: 云南省昆明市盘龙区沣源路452号云南农业大学

description: Library name: Br19_1


title: Chow liver 1


title: KO10_global KO


title: PA-02

value: peripheral blood mononuclear cells


title: Chow liver 4


title: KO6_global KO


title: WT4_control


title: Human CRISPR Knockout Pooled Library (Brunello), SortedB

city: Worcester

first: Junhui

last: Li

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

description:
Library name: SortedB
sample name in allgRNAs-stats-sortedBvsUnsorted.txt: count.sortedB.total and count.sortedB.count

data_processing:
The sequences were mapped to the sgRNA sequences in the human Brunello library using Bowtie (version 1.2.2) with the default parameter settings, except for the options -m 1, –best, and -v 3. Statistical analysis was performed using the CRISPRscreen R package, available at https://github.com/LihuaJulieZhu/CRISPRscreen
Supplementary files format and content: count data for each sample, as well as statistical values such as p-value, adjust-p value and odds ratio
Library strategy: CRISPR Screen

growth_protocol: For the genome-wide CRISPR/Cas9 knockout screen, the A673/EWSR1::FLI1tdTomato/EGFP/Cas9 523 reporter cell line was transduced with the Human CRISPR Knockout Pooled Library (Brunello), consisting of ~76,441 sgRNAs targeting 19,114 genes at multiplicity-525 of-infection (MOI) of 0.3. Cells were selected with 2 μg/ml puromycin for 12 days, followed by 3 526 days recovery in the absence of puromycin.

extract_protocol:
Total genomic DNA was extracted from the sorted and unsorted populations, and 20 μg used to prepare a next-generation sequencing (NGS) library
Total genomic DNA was extracted from the sorted  and unsorted populations, and 20 μg used to prepare a next-generation sequencing (NGS) library. In brief, a series of 24 PCR reactions were prepared—each consisting of 10 μl HF Buffer (NEB), 531 1 μl 10 μM forward primer, 1 μl 10 μM reverse primer, 0.5U Phusion Hot Start II polymerase , and 1 μl 10 mM dNTPs, with milli Q water and template added to 50 μl and subjected to the following cycling conditions: 2 minutes at 98°C, 20 cycles of 30 seconds at  98°C, 30 seconds at 60°C, and 30 seconds at 72°C, and 5 minutes at 72°C.The products of all reactions were pooled and 2 μl of this PCR1 product was used in a subsequent PCR2 reaction using primers containing adapters for NGS. The same  PCR protocol was used, but for 15 instead of 20 cycles. PCR products were purified using standard  PCR purification columns, DNA concentrations were measured, and samples were equimolarly pooled.

value: Ewing Sarcoma


title: Human CRISPR Knockout Pooled Library (Brunello), Control

description:
Library name: Unsorted
sample name in allgRNAs-stats-sortedBvsUnsorted.txt: count.unsorted.total and count.unsorted.count

treatment_protocol: transduced with the Human CRISPR Knockout Pooled Library (Brunello)


title: Hi-C Rv3

city: Delhi

first: Rupesh

last: Chaturvedi

state: Delhi

address: School of biotechnology, JNU, Chattarpur

department: School of Biotechnology

country: India

institute: Jawaharlal nehru university

data_processing:
Hi-C data was processed using Hi-C explorer.
Supplementary files format and content: contact matrix file .h5

organism: Mycobacterium tuberculosis H37Rv

source_name: bacterial cell

growth_protocol: M. tuberculosis strains were cultured in 7H9 medium supplemented with ADC enrichment (5% Albumin, 2% dextrose, 0.003% catalase and 0.85% sodium chloride) and 0.05% Tween 80. All the cultures were grown at 37°C with constant shaking at 200 rpm in a biosafety level 3 facilities. OD at 600 nm was measured to monitor growth.

extract_protocol:
Hi-C experiment were conducted in biological replicates using BglII, according to the protocol published by Umbarger. Et al. Molecular cell 2011. Final DNA libraries were purified using pheonopl chloroform method.
NEBNext® UltraTM II DNA Library Prep Kit for Illumina

value: bacterial cell

value: No treatment


title: 43_99_3

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

description: N007098_Cell1_20211110_1039_1Color_IntegratedResult.txt

hyb_protocol: Hybridization was carried out in accordance with the supplier's (3D-Gene®, Toray Industries, Inc ) instructions.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using "Extraction"(Toray Industries, Inc.) .

data_processing:
A positive call of microRNA was a microarray signal of greater than the [mean + 2×standard deviation] of the negative control signals of which the highest and least intense signals were removed. A positive call signal was subtracted from a mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed and was log-transformed on a base-2 logarithm scale.
Normalization of serum microRNA signals across the different microarrays was performed with the internal control correction coefficient (Int-con). Int-con was a mean of three internal control miRNA signals (miR-149-3p, miR-2861, and miR-4463) (1). Each data was normalized based on the value obtained by subtracting Int-Con from 12.6 (average Int-con value, house data). Each data was then multiplied with the microRNA-specific adjustment coefficient that had been previously obtained from the microRNA–specific calibration curve. As a result, each serum microRNA signal was normalized with the ratio to adjusted Int-con.
In 100 probes, 19 miRNAs which will be analyzed (shown in Matrix sheets.)
Other 81 probes are not utilized for this study.
Our data process steps are simply as follows,
1 Background subtraction
2 Average of triplicated spots
3 Normalize the averaged data

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit (Toray Industries, Inc.) in accordance with the manufacturer's instructions.

growth_protocol: Human serum

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

tag: gender

value: male

tag: disease

value: Healthy control

tag: Stage

tag: block in array


title: Hi-C Rv1

tag: genotype


title: 43_99_2

description: N007094_Cell1_20211109_0953_1Color_IntegratedResult.txt

tag: tissue


title: 43_98_3

description: N007102_Cell1_20211110_0942_1Color_IntegratedResult.txt


title: 43_98_1

description: N007086_Cell1_20211105_0940_1Color_IntegratedResult.txt


title: 43_98_2

description: N007097_Cell1_20211109_1026_1Color_IntegratedResult.txt


title: 43_97_1

description: N007082_Cell1_20211105_1037_1Color_IntegratedResult.txt


title: 43_99_1

description: N007080_Cell1_20211105_1036_1Color_IntegratedResult.txt


title: 43_97_2

description: N007093_Cell1_20211109_0952_1Color_IntegratedResult.txt


title: 43_96_2

description: N007096_Cell1_20211109_1025_1Color_IntegratedResult.txt

value: female


title: 43_95_3


title: 43_96_3

description: N007101_Cell1_20211110_0941_1Color_IntegratedResult.txt


title: 43_95_2


title: Hi-C Rv2

tag: treatment


title: 43_94_3


title: 43_95_1


title: SFT2

type: genomic

city: San Francisco

first: David

last: Raleigh

address: 500 Parnassus

institute: UCSF

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: noob normalization

source_name: FFPE

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FFPE tissue using the Qiagen allprep kit

value: Meningeal solitary fibrous tumors


title: 43_94_2


title: 43_94_1

description: N007091_Cell1_20211105_0941_1Color_IntegratedResult.txt


title: 43_97_3

description: N007100_Cell1_20211110_1041_1Color_IntegratedResult.txt


title: 43_92_1

description: N007084_Cell1_20211105_1038_1Color_IntegratedResult.txt


title: 43_91_3


title: 43_91_1


title: 43_91_2

description: N007095_Cell1_20211109_0954_1Color_IntegratedResult.txt


title: 43_90_2


title: 43_90_3

description: N007099_Cell1_20211110_1040_1Color_IntegratedResult.txt


title: 43_90_1


title: SFT3


title: 43_9_2

value: Pancreatic cancer


title: 43_9_3


title: 43_9_1


title: 43_93_1


title: 43_93_3


title: 43_96_1


title: 43_89_3


title: SFT7


title: 43_89_1


title: SFT1


title: 43_92_3


title: SFT4


title: 43_88_2


title: 43_92_2


title: SFT6


title: 43_88_3


title: 43_89_2


title: 43_87_3


title: 43_86_3


title: 43_85_2


title: 43_86_1


title: 43_86_2


title: 43_87_1


title: SFT8


title: 43_84_2


title: 43_84_3


title: 43_84_1


title: 43_83_3


title: 43_83_1


title: 43_83_2


title: 43_87_2


title: 43_82_3


title: 43_85_3


title: 43_88_1


title: 43_82_1


title: 43_81_3


title: 43_82_2


title: SFT5


title: 43_81_2


title: 43_80_3


title: 43_80_1


title: 43_80_2


title: 43_85_1


title: 43_8_3


title: 43_79_3


title: 43_8_1


title: 43_8_2


title: 43_79_2


title: 43_78_3


title: 43_78_2


title: 43_79_1


title: 43_78_1


title: 43_77_2


title: 43_76_3


title: 43_76_1


title: 43_77_3


title: 43_76_2


title: 43_77_1


title: 43_75_3


title: 43_75_2


title: 43_74_3


title: 43_81_1


title: 43_75_1


title: 43_73_3


title: 43_74_2


title: 43_74_1


title: 43_73_1


title: 43_73_2


title: 43_72_3


title: 43_72_2


title: 43_72_1


title: 43_71_2


title: 43_70_3


title: 43_70_2


title: 43_7_3

value: Biliary cancer


title: 43_69_2


title: 43_7_1


title: 43_69_1


title: 43_68_1


title: 43_68_2


title: 43_67_3


title: 43_67_1


title: 43_66_3


title: 43_66_1


title: 43_65_3


title: 43_64_3


title: 43_66_2


title: 43_64_1


title: 43_71_3


title: 43_67_2


title: 43_63_3


title: 43_63_2


title: 43_63_1


title: 43_62_3


title: 43_65_1


title: 43_71_1


title: 43_70_1


title: 43_62_2


title: 43_7_2


title: 43_64_2


title: 43_62_1


title: 43_61_3


title: 43_61_2


title: 43_68_3


title: 43_60_3


title: 43_61_1


title: 43_6_3


title: 43_60_1


title: 43_59_3


title: 43_6_1


title: 43_6_2


title: 43_65_2


title: 43_59_2


title: 43_59_1


title: 43_57_3


title: 43_58_3


title: 43_58_1


title: 43_57_1


title: 43_56_2


title: 43_56_1


title: 43_55_3


title: 43_55_2


title: 43_56_3


title: 43_54_2


title: 43_54_3


title: 43_53_2


title: 43_60_2


title: 43_53_1


title: 43_54_1


title: 43_50_3


title: 43_50_1


title: 43_50_2


title: 43_5_3


title: 43_5_2


title: 43_58_2


title: 43_5_1


title: 43_49_3


title: 43_49_1


title: 43_93_2


title: 43_57_2


title: 43_49_2


title: 43_47_3


title: 43_46_2


title: 43_47_2


title: 43_46_3


title: 43_46_1


title: 43_55_1


title: 43_47_1


title: 43_4_3


title: 43_51_3


title: 43_4_1


title: 43_51_2


title: 43_4_2


title: 43_34_3


title: 43_53_3


title: 43_35_2


title: 43_35_1


title: 43_51_1


title: 43_35_3


title: 43_34_2


title: 43_33_1


title: 43_33_3


title: 43_33_2


title: 43_32_3


title: 43_32_2


title: 43_32_1


title: 43_31_3


title: 43_31_1


title: 43_31_2


title: 43_30_2


title: 43_30_1


title: 43_30_3


title: 43_3_3


title: 43_3_1


title: 43_29_2


title: 43_29_3


title: 43_27_3


title: 43_28_3


title: 43_28_1


title: 43_23_3


title: 43_27_1


title: 43_26_3


title: 43_26_2


title: 43_34_1


title: 43_3_2


title: 43_23_2


title: 43_26_1


title: 43_23_1


title: 43_22_3


title: 43_29_1


title: 43_27_2


title: 43_22_2


title: 43_22_1


title: 43_21_3


title: 43_21_2


title: 43_21_1


title: 43_20_3


title: 43_2_3


title: 43_20_1


title: 43_20_2


title: 43_2_2


title: 43_19_3


title: 43_19_2


title: 43_18_3


title: 43_2_1


title: 43_18_2


title: 43_18_1


title: 43_17_3


title: 43_19_1


title: 43_17_2


title: 43_16_1


title: 43_16_3


title: 43_17_1


title: 43_15_2


title: 43_15_3


title: 43_16_2


title: 43_14_3


title: 43_14_2


title: 43_14_1


title: 43_15_1


title: 43_12_2


title: 43_12_3


title: 43_12_1


title: 43_113_3


title: 43_113_2


title: 43_113_1


title: 43_112_2


title: 43_112_1


title: 43_111_2


title: 43_111_3


title: 43_110_3


title: 43_110_2


title: 43_112_3


title: 43_110_1


title: 43_111_1


title: 43_11_3


title: 43_11_2


title: 43_11_1


title: 43_107_3


title: 43_107_1


title: 43_106_1


title: 43_105_2


title: 43_106_3


title: 43_107_2


title: 43_105_3


title: 43_104_1


title: 43_105_1


title: 43_104_3


title: 43_104_2


title: 43_106_2


title: 43_103_2


title: 43_103_3


title: 43_28_2


title: 43_102_2


title: 43_101_3


title: 43_102_3


title: 43_101_2


title: 43_103_1


title: 43_100_3


title: 43_102_1


title: 43_100_2


title: 43_100_1


title: 43_10_1


title: 43_1_3


title: 43_1_2


title: 43_10_3


title: 20_768_3

description: N007079_Cell1_20211015_0941_1Color_IntegratedResult.txt


title: 43_1_1


title: 20_766_3

description: N007077_Cell1_20211015_0940_1Color_IntegratedResult.txt


title: 20_768_1

description: N007044_Cell1_20211012_0939_1Color_IntegratedResult.txt


title: 20_767_1

description: N007041_Cell1_20211012_1040_1Color_IntegratedResult.txt


title: 20_767_3

description: N007060_Cell1_20211015_1044_1Color_IntegratedResult.txt


title: 20_768_2

description: N007054_Cell1_20211014_1024_1Color_IntegratedResult.txt


title: 20_766_2

description: N007057_Cell1_20211014_1025_1Color_IntegratedResult.txt


title: 20_765_3

description: N007059_Cell1_20211015_1043_1Color_IntegratedResult.txt


title: 20_766_1


title: 20_765_2

description: N007053_Cell1_20211014_0953_1Color_IntegratedResult.txt


title: 20_764_3


title: 20_765_1

description: N007042_Cell1_20211012_1041_1Color_IntegratedResult.txt


title: 20_764_2


title: 20_763_3


title: 20_763_2

description: N007046_Cell1_20211014_0951_1Color_IntegratedResult.txt


title: 43_101_1


title: 20_763_1


title: 20_762_3


title: 43_10_2

description: N007097_Cell1_20211109_1026_1Color_IntegratedResult.txt


title: 20_762_1


title: 20_762_2


title: 20_761_2


title: 20_761_1


title: 20_760_2


title: 20_760_1


title: 20_759_3

description: N007076_Cell1_20211015_1045_1Color_IntegratedResult.txt


title: 20_767_2

description: N007052_Cell1_20211014_0952_1Color_IntegratedResult.txt


title: 20_759_2


title: 20_759_1


title: 20_758_3


title: 20_758_2


title: 20_758_1

description: N007043_Cell1_20211012_1042_1Color_IntegratedResult.txt


title: 20_764_1


title: 20_757_2


title: 20_756_3


title: 20_757_1


title: 20_756_2


title: 20_755_3


title: 20_756_1

description: N007045_Cell1_20211012_0940_1Color_IntegratedResult.txt


title: 20_755_2


title: 20_754_3


title: 20_755_1


title: 20_754_2


title: 20_754_1


title: 20_761_3


title: 20_753_1


title: 20_753_2


title: 20_760_3


title: 20_752_1


title: 20_752_2


title: 20_751_3


title: 20_751_2


title: 20_751_1


title: 20_750_3


title: 20_750_2


title: 20_749_3


title: 20_750_1


title: 20_757_3


title: 20_749_2


title: 20_748_3


title: 20_749_1


title: 20_747_3


title: 20_747_2


title: 20_746_2


title: 20_745_3


title: 20_753_3


title: 20_745_2


title: 20_745_1


title: 20_744_3


title: 20_752_3


title: 20_744_2


title: 20_744_1


title: 20_743_1


title: 20_743_3


title: 20_743_2


title: 20_742_3


title: 20_742_2


title: 20_742_1


title: 20_741_3


title: 20_741_2


title: 20_748_1


title: 20_740_3


title: 20_740_1


title: 20_748_2


title: 20_747_1


title: 20_739_2


title: 20_739_3


title: 20_740_2


title: 20_739_1


title: 20_738_3


title: 20_746_1


title: 20_746_3


title: 20_738_1


title: 20_737_3


title: 20_737_2


title: 20_737_1


title: 20_738_2


title: 20_736_3


title: 20_736_2


title: 20_736_1


title: 20_735_3


title: 20_735_2


title: 20_390_1

description: N006977_Cell1_20210928_1107_1Color_IntegratedResult.txt


title: 20_388_3

description: N007021_Cell1_20211005_1109_1Color_IntegratedResult.txt


title: 20_388_2

description: N007003_Cell1_20210929_1009_1Color_IntegratedResult.txt


title: 20_741_1


title: 20_387_3

description: N007028_Cell1_20211006_1058_1Color_IntegratedResult.txt


title: 20_388_1

description: N006981_Cell1_20210928_1109_1Color_IntegratedResult.txt


title: 20_735_1

description: N007041_Cell1_20211012_1040_1Color_IntegratedResult.txt


title: 20_387_2

description: N007008_Cell1_20211001_1012_1Color_IntegratedResult.txt


title: 20_387_1

description: N006990_Cell1_20210929_1116_1Color_IntegratedResult.txt


title: 20_385_3

description: N007035_Cell1_20211008_1054_1Color_IntegratedResult.txt


title: 20_384_3

description: N007017_Cell1_20211005_1106_1Color_IntegratedResult.txt


title: 20_386_1

description: N007016_Cell1_20211001_1107_1Color_IntegratedResult.txt


title: 20_384_2


title: 20_385_2


title: 20_384_1


title: 20_383_2

description: N007001_Cell1_20210929_1008_1Color_IntegratedResult.txt


title: 20_385_1

description: N006993_Cell1_20210928_1008_1Color_IntegratedResult.txt


title: 20_383_1


title: 20_383_3

description: N007019_Cell1_20211005_1108_1Color_IntegratedResult.txt


title: 20_386_2


title: 20_382_3


title: 20_382_1

description: N006976_Cell1_20210928_1106_1Color_IntegratedResult.txt


title: 20_381_2


title: 20_382_2

description: N006998_Cell1_20210929_1006_1Color_IntegratedResult.txt


title: 20_381_1

description: N006987_Cell1_20210929_1115_1Color_IntegratedResult.txt


title: 20_380_3

description: N007029_Cell1_20211006_1059_1Color_IntegratedResult.txt


title: 20_380_1


title: 20_379_2


title: 20_379_1

description: N006996_Cell1_20210928_1010_1Color_IntegratedResult.txt


title: 20_378_3

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