title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis13

status: Public on May 03 2021

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

data_processing:
CellRanger version 3.1 (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v3.0).
Seurat R package (version 3.0, https://satijalab.org/seurat/) was used for the single-cell data integration. We first merged single-cell data of samples with the common disease status (psoriasis or control) and the identical reagent kit version (V2.0 or V3.0) into three groups: (1) psoriasis samples with reagent kit V2.0 - 10 samples, (2) psoriasis samples with reagent kit V3.0 - 3 samples, and (3) control samples with reagent kit V2.0 - 5 samples. To harmonize merged groups into a single dataset without batch effects, correspondences between cells in three merged datasets were identified by the FIndIntegrationAnchors function, and used for data integration with the IntegratedData function in Seurat R package.
Principal component analysis and graph-based clustering analysis were performed with Seurat R package (version 3.0, https://satijalab.org/seurat/). Twenty principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) for Dimension Reduction. With a resolution of 0.8, cells were clustered by the FindClusters function. Then, differentially expressed genes of each cluster compared to all other cells were found by the FindAllMarkers function. Differentially expressed genes between psoriasis and control within each cluster were found by the FindMarkers function. The average gene expression of psoriasis vs. control cells within a cluster was calculated by the AverageExpression function.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcode table, gene table and gene expression matrix files generated by Cell Ranger version 3.1.

source_name: Skin biopsy from a psoriasis patient

extract_protocol:
6 mm punch skin biopsy tissues from 13 psoriasis patients and 5 healthy volunteers were bisected, and one of the two bisected skin tissues was incubated in culture medium for harvesting emigrating cells. Harvested skin tissue was immediately placed in 0.2% Dispase II (Sigma-Aldrich) and incubated in a humidified incubator at 37oC and 10% CO2 for 3 hours. Then, epidermis and dermis were separated with forceps and sliced into small pieces with #10 blade scalpels. Epidermis and dermis were separately cultured in RPMI-1640 medium with L-glutamine (Cytiva) supplemented with 10% human albumin serum (Sigma-Aldrich) and without any enzyme or antibiotic agent in a humidified incubator at 37oC and 5% CO2. Nonplastic adherent cells that had emigrated out of epidermis and dermis were harvested after 48 hours. The harvested cells from epidermis and dermis were combined and filtered through a 40-µm cell strainer (Corning) and stored on ice.
The 10x Genomics Chromium Single Cell 3′ Reagents Kit user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep) was used to prepare the single cell suspension. The appropriate volume of each sample was diluted to recover 5,000-10,000 cells. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell chip. After droplet generation, samples were transferred into PCR tubes and we performed reverse transcription using a ProFlex PCR Thermocycler System (Applied Biosystems). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide.

tag: disease state

value: Psoriasis

tag: cell dissociation

tag: treatment

value: untreated

value: Skin biopsy


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis11

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis09


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis07


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis05


title: Human_Skin_Psoriasis_Enzyme_digestion_method, Psoriasis06F


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis10


title: PRO-seq_20h_SE_Biorep1_Tech_2

status: Public on Jun 03 2021

city: Staten Island

first: Cesar

last: Arenas-Mena

state: New York

address: 2800 Victory Boulevard

department: Biology

institute: CSI CUNY

data_processing:
proseq2.0 default parameters https://github.com/Danko-Lab/proseq2.0
Genome_build: Sp3.1
Supplementary_files_format_and_content: 20h_TOTAL_Sep2020_plus3.rpm.bw and 20h_TOTAL_Sep2020_minus3.rpm.bw, bigwig files for the combinned signal from all replicates
Supplementary_files_format_and_content: 20hTOTAL_sep2020.dREG.peak.prob.bed.gz, bed file dREG predictions based on the total signal from all replicates

organism: Strongylocentrotus purpuratus

source_name: 20 hour hatching blastula embryos

growth_protocol: 15 degrees Celsius

extract_protocol:
Density gradient nuclear prep
Chu et al., 2018. PMCID: PMC6204104
PRO-seq

value: embryo


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis08


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis02


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis06


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis03


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis01


title: PRO-seq_20h_SE_Biorep4


title: Human_Skin_Psoriasis_Enzyme_digestion_method, Psoriasis03F


title: Glucose_rep_D1

status: Public on May 17 2021

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.38 and rRNA reads were filtered using SortmeRNA v. 2.0.
QC reads were mapped into the Xanthomonas citri pv. citri str. 306 genome using Bowtie2 algorithm.
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparison against the control (Glucose) condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the control condition (Glucose) were determined by applying p-ajusted ≤ 0.05 as the threshold.
Genome_build: Xanthomonas
Genome_build: European Nucleotide Archive ASM716v1
Genome_build: genome-build-accession GCA_000007165.1
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results

organism: Xanthomonas citri pv. citri

source_name: Bacterial culture

growth_protocol: X. citri was cultivated in LB-medium without sodium chloride (LB ON) with 100 µg/mL of ampicillin, being maintained at 30 °C and 200 rpm for 16 hours. The bacterial cultures were centrifuged and washed with XVM2m medium once, and then inoculated in the XVM2m medium containing glucose or xylooligosaccharides as sole carbohydrate source with an initial optical density at 600 nm of 0.01. Bacteria were grown with constant shaking at 200 rpm and 30 °C and were harvested when reached the mid-exponential phase.

extract_protocol:
RNA was harvested from X. citri cultures at mid-exponential phase using the Trizol/chloroform protocol.  Genomic DNA was then removed, followed by purification of the samples with the RNeasy Mini Kit (Qiagen). Then, 2-2.5 µg of RNA was used for depletion of rRNA using the Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria - Epicenter Biotechnologies).
The preparation of the cDNA libraries was achieved with the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol.  Libraries were sequenced on the Illumina HiSeq 2500.

tag: strain

tag: carbon source

value: Glucose

tag: biological replicate


title: Human_Skin_Normal_Control_Emigrating_cells_method, Control05

source_name: Skin biopsy from a healthy volunteer

value: Control


title: Human_Skin_Normal_Control_Enzyme_digestion_method, Control05F


title: Human_Skin_Normal_Control_Emigrating_cells_method, Control03


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis04


title: Human_Skin_Normal_Control_Emigrating_cells_method, Control01


title: Human_Skin_Normal_Control_Emigrating_cells_method, Control02


title: Human_Skin_Normal_Control_Emigrating_cells_method, Control04


title: Human_Skin_Psoriasis_Emigrating_cells_method, Psoriasis12


title: Human_Skin_Psoriasis_Enzyme_digestion_method, Psoriasis02F


title: Human_Skin_Psoriasis_Enzyme_digestion_method, Psoriasis04F


title: SKOV3_PLNCX2-ITGBL1_rep2

status: Public on Feb 03 2021

type: RNA

city: Gliwice

first: Alexander

middle: Jorge

last: Cortez

state: Silesia

address: Wybrzeze Armii Krajowej 15

department: Department of Biostatistics and Bioinformatics

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch

description: Gene expression data from SKOV3 cells stably transduced with PLNCX2-ITGBL1 construct

hyb_protocol: Following fragmentation, 5.5 ug of ss-cRNA were hybridized to the GeneChip™ Human Transcriptome Array 2.0 (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.  All GeneChips were visually inspected for irregularities. Quality measures, such as the percentage of present genes and the ratio of endogenous genes, indicated a high overall quality of samples and assays.

data_processing: The data were analyzed with Bioconductor package and preprocessed with Robust Multi-Array Average (RMA) with default normalization parameters. Custom CDF environment was used to extract data (Brainarray Version 23.0.0, hta20hsentrezg).

label: biotin

source_name: PLNCX2-ITGBL1-transduced SKOV3 cells

label_protocol: Total RNA (10 ng) from each sample was used as a template for cDNA and subsequent cRNA and 2nd-cycle cDNA syntheses using the GeneChip™ WT Pico Kit (Thermo Fisher Scientific, Waltham, MA, USA). Quality of cRNA was evaluated using 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Twenty µg were taken for 2nd-cycle cDNA synthesis. 5.5 ug ss-cDNA was fragmented and biotinylated according to protocol recommended by manufacturer.

growth_protocol: SKOV3 cells were maintained in McCoy’s medium (Sigma-Aldrich, Saint Louis, MO, USA), OAW42 cells were grown in RPMI (Sigma-Aldrich, Saint Louis, MO, USA) medium supplemented with 0.1% insulin (Sigma-Aldrich). Cell cultures were performed with addition of 10% fetal bovine serum (Gibco, Carlsbad, CA, USA), 100 µg/mL streptomycin and 100 U/mL penicillin (Sigma-Aldrich), at 37 ◦C, in a humidified environment of 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from the cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) with simultaneous on column DNase I digestion, according to the manufacturer’s instructions. RNA quality was assessed using the 2100 Bioanalyzer with the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA) and only samples with RNA integrity number (RIN) > 7.0 were used.

treatment_protocol: Retroviruses were produced by transfecting plasmids (pLNCX2-ITGBL1 or empty pLNCX2) into PT67 packaging cells, according to the manufacturer’s instructions (Retroviral Gene Transfer Technology, Clontech, Takara Bio, Mountain View, CA, USA). OAW42 and SKOV3 cells (2 × 105/6-cm φ dishes) were transduced at 24 h after plating with supernatants containing retroviruses for 24 h at 37 °C with the addition of 8 µg/mL polybrene (Sigma-Aldrich, Saint Louis, MO, USA). Then, culture medium was replaced with the fresh one. This procedure was repeated three times. Stable cell lines which survived geneticin selection (G418, Sigma-Aldrich; OAW42–50 µg/mL, SKOV3–100 µg/mL) were used in further experiments.

tag: cell line

tag: genotype


title: MIHIV323

status: Public on Oct 02 2020

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

description:
short name: H323
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality screened and adapter removal using cutadapt (v1.15).
Mapped to GRch38 human genome using HiSat2 (v2.1.0).
Raw gene counts were extracted using featureCounts (v1.6.5, the Subread package).
Gene Raw count matrix and Transcript per Million (TPM) table for samples was generated using custom Perl scripts.
Genome_build: Human GRch38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: TPM_normalized_gene_counts.txt: Matrix table with TPM normalized counts.
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include abundance measurements for each Sample.

source_name: LPMC

extract_protocol:
Qiagen RNeasy Plus kit according to the manufacturer’s instruction.
Lexogen QuantSeq 3’ mRNA-Seq Library Prep kit according to the manufacturer’s instruction.

value: gut biopsy

tag: cell type

value: Lamina propria mononuclear cells (LPMC)

tag: disease

value: HIV-1 infected

value: Untreated


title: MIHIV819

description:
short name: H819
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV683

description:
short name: H683
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV622

description:
short name: H622
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV825

description:
short name: H825
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV594

description:
short name: H594
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV428

description:
short name: H428
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV998

description:
short name: H998
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV965

description:
short name: H965
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV391

description:
short name: H391
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: SKOV3_wild-type_rep2

description: Gene expression data from unmodified SKOV3 cells

source_name: wild-type SKOV3 cells

value: wild-type control


title: OAW42_PLNCX2-empty_rep3

description: Gene expression data from OAW42 cells stably transduced with empty PLNCX2 vector

source_name: empty PLNCX2-transduced OAW42 cells

value: empty PLNCX2-transduced (empty vector control)


title: MIHIV839

description:
short name: H839
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: SKOV3_PLNCX2-ITGBL1_rep1


title: SKOV3_wild-type_rep3


title: SKOV3_PLNCX2-empty_rep3

description: Gene expression data from SKOV3 cells stably transduced with empty PLNCX2 vector

source_name: empty PLNCX2-transduced SKOV3 cells


title: SKOV3_wild-type_rep1


title: SKOV3_PLNCX2-empty_rep2


title: OAW42_wild-type_rep1

description: Gene expression data from unmodified OAW42 cells

source_name: wild-type OAW42 cells


title: OAW42_wild-type_rep2


title: MIHIV648

description:
short name: H648
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: OAW42_PLNCX2-empty_rep2


title: OAW42_PLNCX2-ITGBL1_rep1

description: Gene expression data from OAW42 cells stably transduced with PLNCX2-ITGBL1 construct

source_name: PLNCX2-ITGBL1-transduced OAW42 cells


title: OAW42_wild-type_rep3


title: OAW42_PLNCX2-ITGBL1_rep2


title: SKOV3_PLNCX2-empty_rep1


title: OAW42_PLNCX2-ITGBL1_rep3


title: SKOV3_PLNCX2-ITGBL1_rep3

description: Gene expression data from SKOV3 cells stably transduced with PLNCX2-ITGBL1 construct


title: MIHIV188

description:
short name: H188
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV154

description:
short name: H154
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV307

description:
short name: H307
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV132

description:
short name: H132
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV972

description:
short name: C972
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt

value: Healthy Control


title: MIHIV286

description:
short name: H286
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV914

description:
short name: C914
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV217

description:
short name: H217
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV716

description:
short name: C716
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV947

description:
short name: C947
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV124

description:
short name: H124
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV138

description:
short name: C138
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV255

description:
short name: C255
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV493

description:
short name: C493
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV361

description:
short name: C361
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV278

description:
short name: C278
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV404

description:
short name: C404
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: g399_IFNb

description:
g399b
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality screened and adapter removal using cutadapt (v1.15).
Mapped to GRch38 human genome using HiSat2 (v2.1.0).
Raw gene counts were extracted using featureCounts (v1.6.5, the Subread package).
Gene Raw count matrix and Transcript per Million (TPM) table for samples was generated using custom Perl scripts.
Genome_build: Human GRch38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: gene_counts_TPM_matrix.txt: Matrix table with TPM normalized counts.
Supplementary_files_format_and_content: *_geneCounts.txt: Tab-delimited text files include abundance measurements.

source_name: CD4 T cells

treatment_protocol: Treated with ISRE activity normalized doses of IFNa1, IFNa2, IFNa5, IFNa8, IFNa14, and IFNb, as well as mock treated for 18 hrs.

value: CD4 T cells

value: ISRE activity normalized dose of IFNb

tag: donor


title: MIHIV178

description:
short name: C178
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: MIHIV582

description:
short name: C582
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: OAW42_PLNCX2-empty_rep1

description: Gene expression data from OAW42 cells stably transduced with empty PLNCX2 vector


title: MIHIV708

description:
short name: C708
Raw_gene_counts_matrix.txt
TPM_normalized_gene_counts.txt


title: g399_IFNa14

description:
g399a14
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

value: ISRE activity normalized dose of IFNa14


title: g356_IFNb

description:
g356b
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g392_IFNa14

description:
g392a14
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g399_IFNa8

description:
g399a8
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

value: ISRE activity normalized dose of IFNa8


title: g392_IFNa8

description:
g392a8
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g392_IFNb

description:
g392b
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g356_IFNa14

description:
g356a14
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g399_IFNa5

description:
g399a5
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

value: ISRE activity normalized dose of IFNa5


title: g356_IFNa5

description:
g356a5
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g399_IFNa2

description:
g399a2
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

value: ISRE activity normalized dose of IFNa2


title: g356_IFNa8

description:
g356a8
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g392_IFNa2

description:
g392a2
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g399_IFNa1

description:
g399a1
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

value: ISRE activity normalized dose of IFNa1


title: g356_IFNa2

description:
g356a2
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g399_Mock

description:
g399m
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt

value: Mock


title: g356_IFNa1

description:
g356a1
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g392_Mock

description:
g392m
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g392_IFNa5

description:
g392a5
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g356_Mock

description:
g356m
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: g392_IFNa1

description:
g392a1
Raw_gene_counts_matrix.txt
gene_counts_TPM_matrix.txt


title: P58-2: hTERT-FH-B, passage 58, biological rep2

status: Public on Jul 11 2020

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: gene expression data from hTERT transgenic hepatocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affy Gene Chip Scanner 3000 7G.

data_processing: The probe level intensities were adjusted by quantile normalization and gene expression measures were summarized by the robust multi-array analysis (RMA) approach with Bioconductor software

source_name: Passage 58 cultured hepatocytes transduced with hTERT gene

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured according to Wege H. et al. Gastroenterology 2003; 124:432-444.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were not specifically treated other than immortalization.

value: fetal liver hepatocytes


title: P58-3: hTERT-FH-B, passage 58, biological rep3


title: P8A: fetal  hepatocytes in the 8th passage, biological rep1

description: gene expression data from cultured fetal hepatocytes

source_name: Passage 8 freshly isolated hepatocytes


title: P58-1: hTERT-FH-B, passage 58, biological rep1


title: P1C: fetal  hepatocytes in the 1st passage, biological rep3

source_name: Passage 1 freshly isolated hepatocytes


title: P22-3: hTERT-FH-B, passage 22, biological rep3

source_name: Passage 22 cultured hepatocytes transduced with hTERT gene


title: Ligase1-K126A-chase-2h

status: Public on Jun 26 2020

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

description: Enrich EdU-labeled DNA, add hairpin, and BS-seq

library_source: genomic

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

molecule: genomic DNA

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 2 hr

growth_protocol: HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.

extract_protocol:
Harvest cells and extract DNA with phenol-chloroform.
Fragment DNA with sonication (Covaris M200) or restrictive enzyme AluI (NEB, R0137). Size select DNA fragments ranging from 100 bp to 200 bp with AMPure beads (1.05X to 2.8X) (Beckman, A63881). Click it reaction to conjugate biotin to EdU labeled DNA: (Tris pH7.5 buffer 15 mM; Biotin azide (Sigma, 762024) 400 uM; CuSO4 (Sigma, 209198)/THPTA (Sigma, 762342) mix (1:5) (100 uM: 500 uM); Sodium ascorbate (freshly prepared, Sigma, A4034) 5 mM). Reaction at 34 °C for 20 min. DNA was purified with MinElute PCR purification kit (Qiagen, 28004). The click it reaction system is modified from (1) (2). End repair (NEB, E6050), dA-tailing (NEB, E6053) and adaptor ligation (NEB, E6056). Hairpin adapter and methylated sequencing adapter were pre-mix at the molar ratio of 3:1 before adapter ligation. After ligation, 1.4X AMPure beads were added to remove un-ligated adapters. Dissolve adapter ligated DNA in 1X TE buffer. Incubate DNA with M280 streptavidin beads (Thermo Fisher, 11205D) in 1X Binding & Washing buffer (5 mM Tris-Cl (pH 7.5), 1M NaCl, 0.5 mM EDTA (pH 8.0)) for 20 min. Wash with 1X Binding & Washing buffer containing 0.5% IGEPAL CA-630 (Sigma, I3021) for 6 times, and then wash with ddH2O once. Dissolve beads in 40 ul ddH2O. Perform bisulfite conversion (Qiagen, 59104) with DNA on beads. PCR amplification (KAPA KR0413) with bisulfite converted DNA. PCR product was running on a 2% agarose-gel and the larger band ranging from 300 bp to 400 bp was hairpin-ligated sample. Recover this band with gel-extraction kit (TIANGEN, DP208). Clean up with AMPure beads (0.9X). Dissolve DNA in 0.1X TE buffer. The HAMMER-seq library is ready for Next Generation Sequencing.

treatment_protocol: HeLa-S3 cells were synchronized at G1/S entrance with thymidine/aphidicolin double block (2 mM thymidine (Sigma, T1895) for 18 h; remove thymidine and continue to culture for 9 h; 1ug/ml aphidicolin (Abcam, 38966-21-1) for another 14 h). Remove aphidicolin. Pulse labeling with 20 uM EdU (Thermo Fisher, E10187) for 4 min. Remove EdU and chase with 20 uM thymidine for a series of desired time length (0 min to 24 h).

tag: gender

value: female

tag: developmental stage

value: adult

value: HeLa-S3 with Ligase1-K126A

value: epithelial adenocarcinoma

tag: genotype/variation

value: cervix

value: 31 years


title: P8B: fetal  hepatocytes in the 8th passage, biological rep2


title: P22-2: hTERT-FH-B, passage 22, biological rep2


title: P8C: fetal  hepatocytes in the 8th passage, biological rep3


title: P113-2: hTERT-FH-B, passage 113, biological rep2

source_name: Passage 113 cultured hepatocytes transduced with hTERT gene


title: P113-3: hTERT-FH-B, passage 113, biological rep3


title: P22-1: hTERT-FH-B, passage 22, biological rep1


title: P0B: fetal hepatocytes in initial culture,biological rep2

description: gene expression data from fresh fetal hepatocytes

source_name: Primary culture freshly isolated hepatocytes


title: Ligase1-K126A-chase-5m

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 5 min

value: HeLa-S3 with Ligase1-K126A knock-in


title: P0A: fetal hepatocytes in initial culture,biological rep1


title: MCM2-Y90A-chase-30m

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 30 min

growth_protocol:
HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.
Mouse embryonic stem cells were cultured on gelatin coated dishes in ES culture medium containing DMEM (ThermoFisher 11995), supplemented with 15% fetal bovine serum (Hyclone 30070.03), 1% None essential amino acids (Merck M7145), 1% L-glutamine (BBI Life Sciences E607004), 0.1% β-mercaptoethanol (Gibco 21985023), 0.01 % LIF (107 U/ml), and 1% Penicillin-Streptomycin (Gibco, 15140122).

tag: strain background

value: Adult female

value: HeLa-S3 with MCM2-Y90A


title: MCM2-Y90A-chase-24h

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 24 hr


title: Ligase1-K126A-chase-30m

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 30 min


title: MCM2-Y90A-chase-5m

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 5 min


title: MCM2-Y90A-chase-0

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 0 min


title: P0C: fetal hepatocytes in initial culture,biological rep3


title: MCM2-Y90A-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
MCM2-c24h-rep

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 24 hr, replicate

growth_protocol:
HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.
Mouse embryonic stem cells were cultured on gelatin coated dishes in ES culture medium containing DMEM (ThermoFisher 11995), supplemented with 15% fetal bovine serum (Hyclone 30070.03), 1% None essential amino acids (Merck􀀂M7145), 1% L-glutamine (BBI Life Sciences􀀂E607004), 0.1% β-mercaptoethanol (Gibco 21985023), 0.01 % LIF (107 U/ml), and 1% Penicillin-Streptomycin (Gibco, 15140122).


title: MCM2-Y90A-chase-2h

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 2 hr


title: P1B: fetal  hepatocytes in the 1st passage, biological rep2


title: Ligase1-K126A-chase-0

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 0 min


title: Ligase1-K126A-chase-24h

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 24 hr


title: MCM2-Y90A-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
MCM2-c2h-rep

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 2 hr, replicate


title: P1A: fetal  hepatocytes in the 1st passage, biological rep1


title: P113-1: hTERT-FH-B, passage 113, biological rep1


title: MCM2-Y90A-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
MCM2-c0-rep

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 0 min, replicate


title: MCM2-Y90A-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
MCM2-Y90A-c5m-rep

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 5 min, replicate


title: Ligase1-K126A-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
Ligase1-K126A-c30m-rep

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 30 min, replicate


title: Ligase1-K126A-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
Ligase1-K126A-c2h-rep

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 2 hr, replicate


title: Ligase1-K126A-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
Ligase1-K126A-c5m-rep

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 5 min, replicate


title: Ligase1-K126A-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
Ligase1-K126A-c0-rep

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 0 min, replicate


title: MCM2-Y90A-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
MCM2-c30m-rep

source_name: EdU labeled MCM2-Y90A HeLa cells with chasing 30 min, replicate


title: Ligase1-K126A-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LIG1-c24h-rep

source_name: EdU labeled Ligase1-K126A HeLa cells with chasing 24 hr, replicate


title: 1week_infected04

status: Public on Jun 01 2020

city: Aachen

first: Mathias

middle: W.

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

country: Germany

institute: RWTH Áachen University

description: Gene expression in total small intestinal tissue after infection

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.   gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

organism: Mus musculus

source_name: total small intestine

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: G. lamblia was cultured in vitro in medium containing (per liter): Trypticase Peptone 20g, Yeast Extract 10g, D (+) Glucose 10g, NaCl 2g, K2HPO4 1g, KH2PO4 0.6g, L-Cysteine 2g, L(+)Ascorbic Acid 0.2g, Ammonium Citrate 22.8mg, Bile 0.5g, Ampicillin (50ug/ml) 50mg, Kanamycin (100ug/ml) 100mg supplemented with 100ml (10%) of heat Inactivated bovine serum (not fetal bovine serum) and adjusted to pH to 7-7.1 using 5M NaOH and filter sterilzed (0.22um) using a vacuum filter. Prior to infection, parasites were put on ice and parasites released from the flask bottom were counted (Neubauer), washed (2000rpm for 5-7 minutes) and adjusted.

extract_protocol: RNA was isolated with Trizol according to the mansufacturer's protocol and stored at -80°C.

treatment_protocol: 3-4 day old neonate mice were orally infected by gavage with 2x105 G. lamblia ATCC 5058 (assemblage B, strain GS, clone H7) trophozoites.

value: C57BL/6J wild type

tag: group

value: infected

tag: agent

value: 2x10^5 G. lamblia ATCC 5058

tag: time after infection

value: 7 days

tag: age

value: 10 days


title: A-ZK94-I1 (LIVER) (12900)

description:
M5711
Gene expression in total liver tissue of infected and of age-matched control animals

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V6.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.
Normalized processed signal intensity values (non-log), averaged across on-chip replicates / quantuplicate measurements. Measurements of control features were removed.

source_name: infected_38 days_total liver tissue

label_protocol: 150 ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

value: 6 weeks

value: 38 days

tag: tissue

value: liver


title: 1week_infected 01

description: Gene expression in total small intestinal tissue in age-matched control animals

tag: strain


title: N-11604-I1 (IEC) (12086)

description: Gene expression in total small intestinal epithellial cells of infected and of age-matched control animals

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: isolated intestinal epithelial cells

extract_protocol: RNA was isolated with Trizol according to the mansufacturer's protocol and stored at -80°C. Intestinal epithelial cells were isolated as described (Lotz et al., JEM, 2006).


title: N-11604-I3 (IEC) (12088)


title: 1week_control02

value: control


title: N-10830-C3 (IEC) (12081)


title: A-ZK487-I3 (LIVER) (12911)

description:
M5713
Gene expression in total liver tissue of infected and of age-matched control animals


title: 1week_infected 02


title: N-10830-C2 (IEC) (12080)


title: A-ZK512-C4 (LIVER) (12904)

description:
M5710
Gene expression in total liver tissue of infected and of age-matched control animals

source_name: control_total liver tissue


title: A-ZK512-C3 (LIVER) (12902)

description:
M5709
Gene expression in total liver tissue of infected and of age-matched control animals


title: A-ZK487-I4 (LIVER) (12913)

description:
M5714
Gene expression in total liver tissue of infected and of age-matched control animals


title: N-10476-C4 (IEC) (11821)


title: 1week_control01


title: 1week_infected03


title: N-11604-I4 (IEC) (12089)


title: 1week_control04


title: A-ZK154-C2 (LIVER) (12897)

description:
M5708
Gene expression in total liver tissue of infected and of age-matched control animals


title: A-ZK509-I2 (LIVER) (12908)

description:
M5712
Gene expression in total liver tissue of infected and of age-matched control animals


title: 1week_control03


title: N-10830-C1 (IEC) (12079)


title: N-ZK152-I1 (LIVER) (12886)

description:
M5703
Gene expression in total liver tissue of infected and of age-matched control animals

source_name: infected_7 days_total liver tissue


title: N-11604-I2 (IEC) (12087)


title: N-ZK152-I2 (LIVER) (12887)

description:
M5704
Gene expression in total liver tissue of infected and of age-matched control animals


title: N-ZK152-I3 (LIVER) (12888)

description:
M5705
Gene expression in total liver tissue of infected and of age-matched control animals


title: N-ZK152-I4 (LIVER) (12889)

description:
M5706
Gene expression in total liver tissue of infected and of age-matched control animals


title: N-ZK166-C4 (LIVER) (12882)

description:
M5702
Gene expression in total liver tissue of infected and of age-matched control animals


title: A-ZK154-C1 (LIVER) (12893)

description:
M5707
Gene expression in total liver tissue of infected and of age-matched control animals


title: N-ZK166-C3 (LIVER) (12881)

description:
M5701
Gene expression in total liver tissue of infected and of age-matched control animals


title: CS13_DA

status: Public on Sep 09 2019

first: Jian

last: He

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

data_processing:
10X Genomics CellRanger version 2.1 were used to the basecalling.
Sequencing data from 10X genomics was processed with CellRanger software package (version 2.1.0) with default mapping arguments. For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to hg19 human transcriptome (UCSC) using Hisat2 (version 2.10). Uniquely mapped reads were counted by HTSeq package83 and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

molecule: polyA RNA

extract_protocol: A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner

value: Dorsal Aorta

tag: development stage


title: CS13_DA_10x

source_name: human embryonic cells


title: CS14_AGM

value: Aorta-Gonad-Mesonephros region


title: 6week_control03

status: Public on Apr 03 2020


title: 6week_infected01

description: Gene expression in total small intestinal tissue after infection


title: 6week_control01


title: 6week_infected02


title: A-10137-C4 (IEC) (11840)


title: 6week_infected03


title: 6week_infected04


title: 6week_control04


title: A-ZK362-I3 (IEC) (12053)


title: CS15_AGM


title: N-ZK166-C1 (LIVER) (12879)

description:
M5699
Gene expression in total liver tissue of infected and of age-matched control animals


title: A-ZK348-C3 (IEC) (12071)


title: A-ZK348-C2 (IEC) (12070)


title: A-ZK348-C1 (IEC) (12069)


title: A-ZK362-I2 (IEC) (12052)


title: A-ZK362-I4 (IEC) (12054)


title: 6week_control02

description: Gene expression in total small intestinal tissue in age-matched control animals


title: TI_26

status: Public on Aug 07 2019

city: Chicago

first: Zhou

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

data_processing:
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19  genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Genome_build: hg19
Supplementary_files_format_and_content: Bed file for each sample with raw reads count summarised to genebody region.

source_name: HCC_tumor adjacent tissue

extract_protocol:
Plasma were separated from blood. the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany) was used to isolate cfDNA. For 26 HCC patients with available cfDNA samples, we also collected their tumors and adjacent tissue samples for comparison. The tissue samples were stored at -80°C after surgical removal. About 10-25 mg of tissue was collected using a scalpel after sample thawing. Genomic DNA (gDNA) was then isolated using the ZR Genomic DNA Tissue Kit (Zymo Research, California, USA). Plasma,10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols. Chemical labeling (5hmc-Seal-seq) [Song, Chun-Xiao, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature biotechnology 29.1 (2011): 68]

tag: tissue subtype

value: tumor adjacent sample


title: TI_25


title: TI_23


title: TI_24


title: TI_22


title: TI_21


title: TI_18


title: TI_19


title: TI_20


title: A-ZK362-I1 (IEC) (12051)

description: Gene expression in total small intestinal epithellial cells of infected and of age-matched control animals


title: PC3-PDEF Rep1

status: Public on Jan 24 2020

city: New Orleans

first: HARI

last: KOUL

state: LA

address: 1700 Tulane Avenue 9th Flor

institute: LSUHSC-NEW ORLEANS-LA

hyb_protocol: Affymetrix Hybridization Protocol.

scan_protocol: Affymetrix Scanning Protocol.

data_processing:
Affymetrix Transcriptome Analysis Console (TAC) Software.
Probe group file: HuGene-1_0-st-v1.r4.pgf
Meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: PC3, PDEF

label_protocol: Affymetrix Labeling Protocol.

growth_protocol: Cells were maintained in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C, 5% CO2 in a humidified incubator.

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: PC3 cells were engineered with empty vector (pBABE), and PDEF over-expression. Cells were snap frozen for subsequent molecular analysis.

tag: cell line

tag: vector


title: TI_16


title: TI_11


title: TI_14


title: TI_12


title: PC3-SCR Rep2

source_name: PC3, control vector


title: PC3-PDEF Rep2


title: TI_5


title: TU_26

value: tumor sample


title: TI_10


title: TI_9


title: TI_13


title: TI_8


title: TI_15


title: TI_7


title: TI_4


title: TI_6


title: TI_3


title: TI_1


title: TU_23


title: TI_2


title: TU_25


title: TU_18


title: TU_22


title: TU_24


title: TU_17


title: TU_12


title: TU_13


title: TU_15


title: TU_14


title: TU_20


title: TU_10


title: TU_9


title: TU_16


title: TU_7


title: TU_4


title: TU_21


title: TU_5


title: TU_3


title: TU_8


title: TU_2


title: TU_1


title: TU_11


title: TU_6


title: TU_19


title: PC3-SCR Rep1


title: TI_17


title: blood_2858

data_processing:
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19  genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for each sample with raw reads count summarised to genebody region.

source_name: Plasma

extract_protocol:
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma

tag: training/validation group


title: blood_2843


title: blood_2835

value: Training


title: blood_2853


title: blood_2839


title: blood_2852


title: blood_2855


title: blood_2836


title: blood_2844


title: blood_2849


title: blood_2860


title: blood_2859


title: blood_2837


title: blood_2834


title: blood_2838


title: blood_2857


title: blood_2841


title: blood_2854


title: blood_2842


title: blood_2846


title: blood_2851


title: blood_2831


title: blood_2833


title: blood_2830


title: blood_2828


title: blood_2827


title: blood_2826


title: blood_2832


title: blood_2822


title: blood_2823


title: blood_2825


title: blood_2817


title: blood_2815


title: blood_2824


title: blood_2819


title: blood_2798


title: blood_2801


title: blood_2802


title: blood_2805


title: blood_2804


title: blood_2814


title: blood_2818


title: blood_2803


title: blood_2806


title: blood_2807


title: blood_2810


title: blood_2809


title: blood_2811


title: blood_2799


title: blood_2796


title: blood_2795


title: blood_2797


title: blood_2794


title: blood_2808


title: blood_2813


title: blood_2793


title: blood_2800


title: N-ZK166-C2 (LIVER) (12880)

description:
M5700
Gene expression in total liver tissue of infected and of age-matched control animals


title: blood_2791


title: blood_2792


title: blood_2790


title: blood_2787


title: blood_2788


title: blood_2785


title: blood_2781


title: blood_2776


title: blood_2777


title: blood_2778


title: blood_2783


title: blood_2784


title: blood_2779


title: blood_2772


title: blood_2774


title: blood_2771


title: blood_2769


title: blood_2765


title: blood_2763


title: blood_2764


title: blood_2760


title: blood_2759


title: blood_2770


title: blood_2762


title: blood_2758


title: blood_2789


title: blood_2782


title: blood_2757


title: blood_2775


title: blood_2755


title: blood_2786


title: blood_2750


title: blood_2753


title: blood_2751


title: blood_2749


title: blood_2747


title: blood_2748


title: blood_2745


title: blood_2744


title: blood_2743


title: blood_2746


title: blood_2741


title: blood_2740


title: blood_2738


title: blood_2735


title: blood_2737


title: blood_2733


title: blood_2730


title: blood_2732


title: blood_2734


title: blood_2731


title: blood_2724


title: blood_2722


title: blood_2727


title: blood_2752


title: blood_2717


title: blood_2756


title: blood_2716


title: blood_2742


title: blood_2715


title: blood_2712


title: blood_2709


title: blood_2711


title: blood_2713


title: blood_2714


title: blood_2707


title: blood_2702


title: blood_2705


title: blood_2710


title: blood_2703


title: blood_2698


title: blood_2696


title: blood_2694


title: blood_2695


title: blood_2699


title: blood_2701


title: blood_2697


title: blood_2693


title: blood_2718


title: blood_2690


title: blood_2692


title: blood_2691


title: blood_2687


title: blood_2706


title: blood_2685


title: blood_2704


title: blood_2686


title: blood_2689


title: blood_2688


title: blood_2684


title: blood_2681


title: blood_2680


title: blood_2682


title: blood_2683


title: blood_2676


title: blood_2677


title: blood_2678


title: blood_2675


title: blood_2674


title: blood_2673


title: blood_2672


title: blood_2671


title: blood_2668


title: blood_2669


title: blood_2667


title: blood_2670


title: blood_2664


title: blood_2665


title: blood_2666


title: blood_2663


title: blood_2662


title: blood_2661


title: blood_2656


title: blood_2657


title: blood_2655


title: blood_2658


title: blood_2659


title: blood_2660


title: blood_2679


title: blood_2653


title: blood_2654


title: blood_2644


title: blood_2648


title: blood_2650


title: blood_2649


title: blood_2647


title: blood_2642


title: blood_2641


title: blood_2637


title: blood_2638


title: blood_2643


title: blood_2640


title: blood_2635


title: blood_2633


title: blood_2634


title: blood_2631


title: blood_2639


title: blood_2651


title: blood_2627


title: blood_2629


title: blood_2630


title: blood_2625


title: blood_2628


title: blood_2645


title: blood_2636


title: blood_2632


title: blood_2626


title: blood_2624


title: blood_2646


title: blood_2620


title: blood_2622


title: blood_2616


title: blood_2615


title: blood_2614


title: blood_2623


title: blood_2613


title: blood_2612


title: blood_2611


title: blood_2609


title: blood_2610


title: blood_2606


title: blood_2608


title: blood_2605


title: blood_2602


title: blood_2599


title: blood_2600


title: blood_2598


title: blood_2594


title: blood_2596


title: blood_2595


title: blood_2618


title: blood_2592


title: blood_2621


title: blood_2597


title: blood_2617


title: blood_2593


title: blood_2591


title: blood_2589


title: blood_2590


title: blood_2588


title: blood_2586


title: blood_2587


title: blood_2607


title: blood_2580


title: blood_2581


title: blood_2584


title: blood_2582


title: blood_2583


title: blood_2578


title: blood_2579


title: blood_2576


title: blood_2575


title: blood_2572


title: blood_2569


title: blood_2573


title: blood_2570


title: blood_2571


title: blood_2567


title: blood_2568


title: blood_2565


title: blood_2563


title: blood_2604


title: blood_2561


title: blood_2559


title: blood_2585


title: blood_2562


title: blood_2560


title: blood_2557


title: blood_2556


title: blood_2555


title: blood_2554


title: blood_2552


title: blood_2553


title: blood_2550


title: blood_2549


title: blood_2577


title: blood_2547


title: blood_2574


title: blood_2545


title: blood_2544


title: blood_2542


title: blood_2546


title: blood_2540


title: blood_2558


title: blood_2537


title: blood_2541


title: blood_2538


title: blood_2539


title: blood_2535


title: blood_2534


title: blood_2536


title: blood_2532


title: blood_2528


title: blood_2527


title: blood_2525


title: blood_2529


title: blood_2551


title: blood_2524


title: blood_2520


title: blood_2519


title: blood_2518


title: blood_2521


title: blood_2516


title: blood_2517


title: blood_2522


title: blood_2514


title: blood_2513


title: blood_2515


title: blood_2511


title: blood_2507


title: blood_2509


title: blood_2531


title: blood_2512


title: blood_2508


title: blood_2526


title: blood_2504


title: blood_2510


title: blood_2505


title: blood_2503


title: blood_2506


title: blood_2523


title: blood_2501


title: blood_2502


title: blood_2497


title: blood_2495


title: blood_2498


title: blood_2496


title: blood_2499


title: blood_2493


title: blood_2492


title: blood_2490


title: blood_2491


title: blood_2489


title: blood_2494


title: blood_2487


title: blood_2485


title: blood_2483


title: blood_2484


title: blood_2482


title: blood_2486


title: blood_2478


title: blood_2481


title: blood_2477


title: blood_2480


title: blood_2479


title: blood_2476


title: blood_2474


title: blood_2475


title: blood_2465


title: blood_2471


title: blood_2488


title: blood_2469


title: blood_2470


title: blood_2466


title: blood_2462


title: blood_2460


title: blood_2461


title: blood_2472


title: blood_2458


title: blood_2464


title: blood_2468


title: blood_2457


title: blood_2456


title: blood_2463


title: blood_2454


title: blood_2450


title: blood_2453


title: blood_2451


title: blood_2452


title: blood_2448


title: blood_2467


title: blood_2446


title: blood_2449


title: blood_2447


title: blood_2445


title: blood_2440


title: blood_2441


title: blood_2443


title: blood_2436


title: blood_2435


title: blood_2442


title: blood_2439


title: blood_2434


title: blood_2437


title: blood_2459


title: blood_2438


title: blood_2455


title: blood_2431


title: blood_2428


title: blood_2429


title: blood_2426


title: blood_2423


title: blood_2430


title: blood_2425


title: blood_2422


title: blood_2421


title: blood_2473


title: blood_2420


title: blood_2424


title: blood_2418


title: blood_2416


title: blood_2417


title: blood_2414


title: blood_2415


title: blood_2411


title: blood_2433


title: blood_2432


title: blood_2407


title: blood_2406


title: blood_2408


title: blood_2409


title: blood_2410


title: blood_2405


title: blood_2403


title: blood_2404


title: blood_2402


title: blood_2401


title: blood_2399


title: blood_2400


title: blood_2395


title: blood_2390


title: blood_2419


title: blood_2396


title: blood_2388


title: blood_2394


title: blood_2412


title: blood_2387


title: blood_2385


title: blood_2393


title: blood_2391


title: blood_2384


title: blood_2383


title: blood_2413


title: blood_2381


title: blood_2379


title: blood_2377


title: blood_2378


title: blood_2376


title: blood_2375


title: blood_2398


title: blood_2373


title: blood_2371


title: blood_2370


title: blood_2369


title: blood_2372


title: blood_2368


title: blood_2367


title: blood_2366


title: blood_2359


title: blood_2364


title: blood_2357


title: blood_2363


title: blood_2360


title: blood_2365


title: blood_2355


title: blood_2356


title: blood_2358


title: blood_2382


title: blood_2353


title: blood_2374


title: blood_2352


title: blood_2351


title: blood_2349


title: blood_2350


title: blood_2348


title: blood_2346


title: blood_2345


title: blood_2347


title: blood_2362


title: blood_2361


title: blood_2343


title: blood_2342


title: blood_2341


title: blood_2338


title: blood_2335


title: blood_2331


title: blood_2334


title: blood_2337


title: blood_2336


title: blood_2340


title: blood_2333


title: blood_2330


title: blood_2332


title: blood_2329


title: blood_2354


title: blood_2325


title: blood_2323


title: blood_2322


title: blood_2319


title: blood_2324


title: blood_2318


title: blood_2321


title: blood_2327


title: blood_2320


title: blood_2328


title: blood_2315


title: blood_2326


title: blood_2314


title: blood_2312


title: blood_2313


title: blood_2316


title: blood_2317


title: blood_2339


title: blood_2344


title: blood_2311


title: blood_2310


title: blood_2307


title: blood_2308


title: blood_2305


title: blood_2309


title: blood_2304


title: blood_2306


title: blood_2303


title: blood_2299


title: blood_2295


title: blood_2302


title: blood_2289


title: blood_2288


title: blood_2298


title: blood_2296


title: blood_2293


title: blood_2300


title: blood_2290


title: blood_2287


title: blood_2282


title: blood_2291


title: blood_2285


title: blood_2297


title: blood_2284


title: blood_2280


title: blood_2278


title: blood_2279


title: blood_2277


title: blood_2283


title: blood_2273


title: blood_2272


title: blood_2281


title: blood_2275


title: blood_2294


title: blood_2286


title: blood_2268


title: blood_2270


title: blood_2269


title: blood_2261


title: blood_2255


title: blood_2259


title: blood_2266


title: blood_2267


title: blood_2260


title: blood_2254


title: blood_2256


title: blood_2246


title: blood_2252


title: blood_2276


title: blood_2274


title: blood_2257


title: blood_2243


title: blood_2242


title: blood_2253


title: blood_2238


title: blood_2237


title: blood_2247


title: blood_2244


title: blood_2271


title: blood_2263


title: blood_2236


title: blood_2235


title: blood_2234


title: blood_2249


title: blood_2232


title: blood_2233


title: blood_2231


title: blood_2222


title: blood_2224


title: blood_2218


title: blood_2220


title: blood_2221


title: blood_2225


title: blood_2226


title: blood_2223


title: blood_2213


title: blood_2217


title: blood_2214


title: blood_2215


title: blood_2210


title: blood_2216


title: blood_2209


title: blood_2211


title: blood_2212


title: blood_2240


title: blood_2207


title: blood_2206


title: blood_2204


title: blood_2202


title: blood_2228


title: blood_2203


title: blood_2199


title: blood_2194


title: blood_2200


title: blood_2196


title: blood_2198


title: blood_2193


title: blood_2195


title: blood_2197


title: blood_2191


title: blood_2192


title: blood_2208


title: blood_2187


title: blood_2185


title: blood_2186


title: blood_2188


title: blood_2184


title: blood_2189


title: blood_2183


title: blood_2182


title: blood_2205


title: blood_2179


title: blood_2177


title: blood_2180


title: blood_2201


title: blood_2181


title: blood_2178


title: blood_2176


title: blood_2190


title: blood_2175


title: blood_2172


title: blood_2173


title: blood_2169


title: blood_2168


title: blood_2171


title: blood_2166


title: blood_2167


title: blood_2165


title: blood_2164


title: blood_2161


title: blood_2160


title: blood_2157


title: blood_2163


title: blood_2159


title: blood_2156


title: blood_2154


title: blood_2155


title: blood_2152


title: blood_2151


title: blood_2150


title: blood_2174


title: blood_2153


title: blood_2170


title: blood_2149


title: blood_2148


title: blood_2145


title: blood_2143


title: blood_2147


title: blood_2146


title: blood_2142


title: blood_2144


title: blood_2158


title: blood_2141


title: blood_2139


title: blood_2140


title: blood_2136


title: blood_2137


title: blood_2138


title: blood_2135


title: blood_2134


title: blood_2132


title: blood_2131


title: blood_2130


title: blood_2128


title: blood_2127


title: blood_2129


title: blood_2126


title: blood_2125


title: blood_2123


title: blood_2112


title: blood_2120


title: blood_2113


title: blood_2122


title: blood_2114


title: blood_2133


title: blood_2111


title: blood_2115


title: blood_2118


title: blood_2110


title: blood_2109


title: blood_2117


title: blood_2105


title: blood_2106


title: blood_2108


title: blood_2107


title: blood_2104


title: blood_2103


title: blood_2099


title: blood_2097


title: blood_2098


title: blood_2100


title: blood_2095


title: blood_2096


title: blood_2119


title: blood_2090


title: blood_2088


title: blood_2087


title: blood_2086


title: blood_2089


title: blood_2085


title: blood_2084


title: blood_2082


title: blood_2083


title: blood_2078


title: blood_2080


title: blood_2081


title: blood_2102


title: blood_2101


title: blood_2079


title: blood_2074


title: blood_2073


title: blood_2072


title: blood_2071


title: blood_2069


title: blood_2070


title: blood_2067


title: blood_2068


title: blood_2066


title: blood_2065


title: blood_2064


title: blood_2076


title: blood_2077


title: blood_2062


title: blood_2061


title: blood_2075


title: blood_2050


title: blood_2055


title: blood_2057


title: blood_2051


title: blood_2230


title: blood_2058


title: blood_2052


title: blood_2047


title: blood_2054


title: blood_2229


title: blood_2049


title: blood_2048


title: blood_2053


title: blood_2043


title: blood_2044


title: blood_2046


title: blood_2245


title: blood_2042


title: blood_2063


title: blood_2045


title: blood_2041


title: blood_2040


title: blood_2056


title: blood_2039


title: blood_2038


title: blood_2037


title: blood_2036


title: blood_2027


title: blood_2028


title: blood_2030


title: blood_2031


title: blood_2026


title: blood_2024


title: blood_2018


title: blood_2019


title: blood_2014


title: blood_2015


title: blood_2013


title: blood_2012


title: blood_2033


title: blood_2008


title: blood_2009


title: blood_2007


title: blood_2006


title: blood_2011


title: blood_2034


title: blood_2010


title: blood_2005


title: blood_2003


title: blood_2001


title: blood_2000


title: blood_2020


title: blood_2004


title: blood_2017


title: blood_1999


title: blood_1998


title: blood_1997


title: blood_2002


title: blood_1996


title: blood_2016


title: blood_1994


title: blood_1993


title: blood_1995


title: blood_1992


title: blood_1990


title: blood_1988


title: blood_1989


title: blood_1987


title: blood_1984


title: blood_1986


title: blood_1983


title: blood_1985


title: blood_1982


title: blood_1980


title: blood_1991


title: blood_1981


title: blood_1978


title: blood_1976


title: blood_1975


title: blood_1977


title: blood_1972


title: blood_1974


title: blood_1971


title: blood_1970


title: blood_1969


title: blood_1967


title: blood_1968


title: blood_1973


title: blood_1962


title: blood_1966


title: blood_1961


title: blood_1960


title: blood_1965


title: blood_1957


title: blood_1956


title: blood_1955


title: blood_1954


title: blood_1953


title: blood_1951


title: blood_1950


title: blood_1952


title: blood_1949


title: blood_2025


title: blood_1945


title: blood_1947


title: blood_1946


title: blood_1948


title: blood_1942


title: blood_1943


title: blood_1941


title: blood_1964


title: blood_1938


title: blood_1944


title: blood_1939


title: blood_1958


title: blood_1936


title: blood_1933


title: blood_1934


title: blood_1935


title: blood_1931


title: blood_1930


title: blood_1927


title: blood_1928


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