title: AP sites, U plasmid DNA treated with Udg

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: Library name: AP_U_plasmid_Udg

library_source: other

data_processing:
After demultiplexing of sequencing data, each sample was represented by a fastq.gz file containing 101-nucleotide-long genomic reads. The quality of the raw sequencing data was checked via FastQC version 0.12.1. Low-quality reads and adapter-containing reads were removed via trimmomatic version 0.39. We retained only those reads that contained a validation code (VC). The first 17 nucleotides corresponding to VC and randomized index code (RIC) were clipped from the read sequences and appended to the read names via the tool extract of umi_tools toolkit version 1.1.4. In case of samples from cells, reads were mapped to human reference genome GRCh38 via bowtie2 version 2.5.1, using pre-built bowtie2 index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip, and applying otherwise standard settings. In case of samples originating from plasmids, we built bowtie2 indexes for three plasmids, namely, i) input plasmid (vector), ii) plasmid with triple 8-oxoG insert, 8-oxoG represented by G, and iii) plasmid with triple U insert, U represented by T (triple insert explained in the article's Extended Data Fig. 2g); the plasmid sequences were flanked by 100 nucleotides to mimic circular structure in read alignment; these indexes were used to map reads via bowtie2 2.5.1. Read duplicates were removed by the tool dedup of umi_tools toolkit version 1.1.4, grouping reads with the same code sequence stored in the read name (method=unique). Samtools version 1.17 were employed to sort, index and generate statistics of bam files. bedtools2 version 2.31.0 were used to retrieve the coordinates of mapped and deduplicated reads and extract the sequence context of DNA modifications from the reference genome. Each read represented one unit of DNA-modification signal, which we positioned at the nucleotide of the 5’ end of the read. Since a read was the reverse complement of the DNA fragment captured in the method employing MoDIS, the strand of the nucleotide bearing the signal was changed to the opposite one. We implemented the described DNA-modification-signal positioning via custom scripts in Python version 3.11.6 [GCC 12.2.0] with modules numpy version 1.25.2, pandas version 2.2.2 and biopython version 1.83.
Library strategy: click-code-seq
Assembly: GRCh38
Supplementary files format and content: In the provided sample-specific tsv-files, each line reflects one DNA modification revealed by one mapped read. The tsv-files contain the following columns: 1) the chromosome, 2) the 0-based coordinate, 3) the strand, 4) the nucleotide bearing the signal, 5) MAPQ score of the read.

molecule: other

organism: Escherichia coli

source_name: BL21 DE3

growth_protocol: HAP1 cells (RRID:CVCL_Y019, Horizon Discovery) were cultivated in Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). U2OS cells (RRID:CVCL_0042) were cultivated in McCoy‘s general cell culture medium, modified with high glucose, L-glutamate, bacto-peptone and phenol red, and lacking sodium pyruvate and HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (McCoy‘s 5A, Gibco 16600082), supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). 10 mL of cell culture medium was supplemented by 4 μL GSK-3484862 (MedChemExpress, 10 mM dissolved in DMSO) (final concentration 4 μM). Control medium was prepared by adding 4 μL of DMSO to 10 mL of cell culture medium. The treatment and control media were filtered with a sterile syringe filter (0.22 μm) and added to the cells, followed by 72-h incubation at 37 °C, 5% CO2, 3% O2, with the treatment and control media being refreshed after every 24 hours. In case of plasmid samples: plasmids containing site-specific 8-oxoG and uracil were constructed by inserting double-stranded oligonucleotides into a 4.7-Kbp plasmid vector via a restriction-ligation strategy. The plasmid pEGFP-W, derived from pEGFP-N1 (Addgene, Catalog Number 6085-1), was purified from BL21 (DE3) E. coli (NEB) using a Qiagen plasmid maxi prep kit (Qiagen, USA) and digested with BamHI-HF (NEB) and HindIII-HF (NEB) restriction enzymes, generating sticky ends for subsequent ligation.

extract_protocol:
In case of HAP1 and U2OS, cells were harvested by removing the medium, washing once with 10 mL DPBS followed by addition of 1 mL 0.25% Trypsin EDTA solution (Gibco). After an incubation of 5 min at 37°C, 9 mL medium was added, cells resuspended and transferred to a Falcon centrifugal tube. Cells were centrifuged (4°C, 0.3 rcf, 5 min) and the supernatant removed. gDNA was extracted from  cell pellets using the Monarch Genomic DNA Extraction Kit following the manufacturer’s instructions. In order to avoid artefactual oxidation, DPBS used in the cell pellet resuspension  was supplemented with 1 mM deferoxamine and 50 µM n-tert-butyl-α-phenylnitrone. In case of the plasmid samples, the input plasmid vector pEGFP-W, derived from pEGFP-N1 (Addgene, Catalog Number 6085-1), was purified from BL21 (DE3) E. coli (NEB) using a Qiagen plasmid maxi prep kit (Qiagen, USA).
To minimize artefactual damage, samples were inverted or flicked, instead of pipette mixing, until the CuAAC step. For DNA oxidation mapping, gDNA was eluted in H2O supplemented with 500 µM 8-hydroxyquinoline (HQ; Sigma) after extraction and purification. Undesired background modifications were blocked by adding 1 µL ENDOIV (NEB, 10 U/µL) and 500 µM 8-HQ to 5 µg of gDNA, freshly extracted from HAP1 pellets, in 1x ThermoPol Buffer (NEB) in a final volume of 20 µL, and incubating the mixture for 20 min at 37°C. 2.5 µL ddNTP mix (Jena Biosciences, 2.5 mM), 0.5 µL 10x ThermoPol Buffer, 1.8 µL of 8-HQ (500 µM) and 0.2 µL Therminator IX (NEB, 10 U/µL) were added, followed by a 10 min incubation at 60°C. 25 µL 8-HQ (500 µM) and 80 µL Pronex® beads were added for purification with an elution volume of 25 µL. To label oxidative modifications, 1 µL FPG (NEB, 8 U/µL), 1 µL ENDOIV (NEB, 10 U/µL) and 3 µL 10x NEBuffer 2 (NEB) were added for a final volume of 30 µL; the reaction mixture was incubated for 1 h at 37°C, immediately followed by adding 3.5 µL prop-dGTP (Jena Biosciences, 2.5 mM), 0.5 µL 10x NEBuffer 2 (NEB), 0.8 µL 8-HQ (500 µM) and 0.2 µL Therminator IX (NEB 10 U/µL) for 10-min incubation at 60°C. As for the plasmid DNA, each modified plasmid was separately spiked into 2 µg of the original pEGFP-W plasmid and subjected to these same initial steps. In the case of the uracil-modified plasmid, UDG (NEB, 5 U/µL) was used instead of FPG to excise the uracil base, and prop-dTTP (Jena Biosciences, 2.5 mM) was used instead of prop-dGTP. Two control samples containing 2 µg of unmodified pEGFP-W plasmid were processed under identical conditions with either FPG and prop-dGTP or UDG and prop-dTTP. Steps for mapping either AP sites or oxidative damage, both for gDNA and plasmid DNA, are identical from this point onwards. DNA was purified using Pronex® Magnetic Beads (Promega) with a sample:bead ratio of 50:80 and using an elution volume of 50 µL with Buffer EB. Sonication of DNA was performed using a Q800R2 sonicator (QSonica) with the following settings: 4°C, 20% amplitude, pulse 15 s on, 5 s off, total 5 min for gDNA and 4 min for plasmid DNA. The resulting DNA fragments were analyzed on a Tapestation 2200 using a High Sensitivity D100 ScreenTape (Agilent Technologies). DNA was purified using Pronex® beads with a sample:beads ratio of 1:2 and 50 µL elution volume. Samples were quantified using a Quantus™ Fluorometer. For adapter ligation, NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) was utilized using either 1 µg of gDNA or the remaining plasmid DNA and the pre-annealed NEB adapter (NEB_P7, NEB_P5, 15 µM; Supplementary Table 1). The manufacturer’s instruction was followed without performing the USER enzyme step. The sample was purified using Pronex® beads in sample:beads ratio 1:2 and elution in 50 µL Buffer EB. Successful adapter ligation was checked on an Agilent TapeStation with a High Sensitivity D100 ScreenTape. The sample volume was then condensed to 6 µL using a vacuum concentrator. To denature DNA, the sample was heated to 95°C for 2 min and rapidly cooled on ice. CuAAC reaction was performed using 2 µL MoDIS (100 µM equimolar mixture of MoDIS_1 and MoDIS_2; Supplementary Table 1), 4 µL DMSO, 2 µL premixed CuSO4:THPTA (THPTA from Lumiprobe; 20 mM Cu2+ and 200 mM THPTA) and 2 µL sodium phosphate buffer (1 M, pH 7.0). The reaction was started by adding 2 µL sodium ascorbate (400 mM in H2O, freshly prepared) and incubated for 60 min at 37°C. Purification was done using Pronex® beads in a sample:beads ratio 1:2 and 30 µL elution volume. Biotin enrichment of sample DNA was performed using Dynabeads™ MyOne™ Streptavidin C1 (ThermoFisher). First, B&W buffer was prepared according to the manufacturer’s protocol including 0.05 % Tween™ 20. Then, 15 µL Dynabeads™ were transferred to a fresh tube, washed three times with 200 µL 1x B&W buffer and resuspended in 30 µL 2x B&W buffer. The DNA sample was denatured by heating to 95°C for 2 min and rapid cooling on ice. Then, 30 µL sample was mixed with 30 µL of the prepared Dynabeads™ and rotated for 15 min at RT. Afterwards, the Dynabeads™ were washed 3x with 1x B&W buffer by resuspending the beads, 3 min rotation and 1 min pelleting on a magnetic rack. A final wash was performed with Buffer EB and Dynabeads™ were resuspended in 20 µL Buffer EB. To amplify the biotin-enriched material, a PCR was performed by adding 5 µL 10x ThermoPol buffer, 5 µL dNTP mix (NEB, 2 mM), 1 µL MgSO4 (100 mM), 1 µL ex_UMI (10 µM; Supplementary Table 1), 1 µL Pr_P7 (10 µM; Supplementary Table 1) and 0.5 µL Vent (exo-) DNA Polymerase (NEB 2 U/µL). The PCR program comprised an initial denaturation step (95°C, 120 s), followed by 5 cycles of denaturation (95°C, 20 s), annealing (59°C, 20 s) and elongation (72°C, 60 s) and a final elongation step (72°C, 300 s). The sample was purified with Pronex® beads in a sample:beads ratio 1:2 and an elution volume of 30 µL. Final library amplification and indexing was performed by adding 25 µL NEBNext® Ultra™ II Q5® Master Mix (NEB), 2.5 µL i5_Index (10 µM; Supplementary Table 1) and 2.5 µL i7_Index (10 µM; Supplementary Table 1) to 20 µL sample. The PCR program comprised an initial denaturation step (98°C, 30 s), 10 cycles of denaturation (98°C, 10 s), annealing (68°C, 30 s) and elongation (72°C, 20 s), and a final elongation step (72°C, 120 s). The same PCR setup can be used for a precedent qPCR by adding a qPCR dye as Evagreen (Biotium) to test for successful sample amplification. The PCR sample was purified with the Pronex® beads dual size selection protocol using an initial sample:beads ratio of 1:1, followed by a sample:beads ratio of 0.5:1 to exclude fragments longer than 1000 bp and shorter than 250 bp. The final sample concentration was adjusted to a concentration of 4 ng/µL and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: In case of DNMT1 inhibition experiment: 10 mL of cell culture medium was supplemented by 4 μL GSK-3484862 (MedChemExpress, 10 mM dissolved in DMSO) (final concentration 4 μM); control medium was prepared by adding 4 μL of DMSO to 10 mL of cell culture medium. In case of plasmid samples, 8-oxoG-inserted plasmid was mixed with the input vecor, and the mixture was treated with FPG to recognize oxidized guanines (as in the DNMT1-inhbition samples within the click-code-seq protocol). For the uracil-modified plasmid, UDG (NEB, 5 U/µL) was used instead of FPG to excise the uracil base. Two control samples containing 2 µg of unmodified pEGFP-W plasmid were processed under identical conditions with either FPG or UDG.

value: BL21 DE3

value: Udg


title: N128

status: Public on Aug 22 2025

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: disease subgroup

value: Mixed

tag: in 300? (yes, no)

value: yes

tag: in 280? (yes, no)


title: Oxidized guanines, vector DNA treated with Fpg

type: SRA

description: Library name: OG_vector_Fpg

tag: cell line

tag: strain

tag: treatment

value: Fpg


title: AP sites, vector DNA treated with Udg

description: Library name: AP_vector_Udg


title: Sample6_RNAseq_Resting2

city: Los Angeles

first: Ping

last: Wu

state: California

address: 2011 Zonal Ave HMR313A

country: USA

institute: University of Southern California

description:
Library name: Sample6
Sample6_RNAseq_Resting2

library_source: transcriptomic

data_processing:
TPM values for each gene were obtained from the mapping files using StringTie (using default parameters)
Assembly: GRCg6a, Ensembl
Supplementary files format and content: The read counts and transcripts per million (TPM)

organism: Gallus gallus

source_name: feather follicle

extract_protocol:
Trizol RNA extraction
TruSeq RNA sample preparation v2 kit (Illumina)

tag: tissue

value: feather follicle

tag: cell type

value: Epidermal progenitor cells

tag: genotype

value: White leghorn chicken

value: No treatment

tag: batch


title: Sample5_RNAseq_Resting1

description:
Library name: Sample5
Sample5_RNAseq_Resting1


title: Sample4_RNAseq_Late_growth2

description:
Library name: Sample4
Sample4_RNAseq_Late_growth2


title: Sample2_RNAseq_Early_growth2

description:
Library name: Sample2
Sample2_RNAseq_Early_growth2


title: Sample1_RNAseq_Early_growth1

description:
Library name: Sample1
Sample1_RNAseq_Early_growth1


title: Sample3_RNAseq_Late_growth1

description:
Library name: Sample3
Sample3_RNAseq_Late_growth1


title: N106

value: Normal


title: N105

value: ABMR


title: N101


title: HP1529801T2D_A1

city: Huddinge

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome hg38 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 40% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; and 4) >= 1000 genes with RPKM >= 1. In addition, doublets detected by Scrublet were further removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell …

source_name: Human pancreatic islet single cells

extract_protocol: The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).

value: Pancreatic islets

tag: disease state


title: HP1529801T2D_C9


title: HP1529801T2D_E12


title: N10


title: N103

value: cAKI


title: N100

value: pTCMR


title: N102


title: N104


title: HP1529801T2D_E7


title: HP1529801T2D_I8


title: HP1529801T2D_A17


title: HP1529801T2D_H6


title: HP1529801T2D_B16


title: HP1529801T2D_A16


title: HP1529801T2D_H2


title: HP1529801T2D_D15


title: HP1529801T2D_I12


title: N16


title: HP1529801T2D_D24


title: HP1529801T2D_K11


title: HP1529801T2D_E6


title: HP1529801T2D_D1


title: N129


title: N1


title: HP1529801T2D_F4


title: N115


title: HP1529801T2D_M23


title: HP1529801T2D_H5


title: Oxidized guanines, 8oxoG plasmid DNA treated with Fpg

description: Library name: OG_8oxoG_plasmid_Fpg


title: HP1529801T2D_I6


title: HP1529801T2D_B22


title: HP1529801T2D_I21


title: HP1529801T2D_G2


title: HP1529801T2D_E19


title: HP1529801T2D_N17


title: HP1529801T2D_A5


title: HP1529801T2D_B15


title: HP1529801T2D_P1


title: HP1529801T2D_C8


title: HP1529801T2D_P24


title: HP1529801T2D_G11


title: HP1529801T2D_M15


title: HP1529801T2D_M16


title: HP1529801T2D_P19


title: HP1529801T2D_I9


title: HP1529801T2D_J21


title: HP1529801T2D_I4


title: HP1529801T2D_J10


title: HP1529801T2D_G20


title: HP1529801T2D_L23


title: HP1529801T2D_L18


title: HP1529801T2D_E2


title: HP1529801T2D_D3


title: HP1529801T2D_C6


title: HP1529801T2D_F19


title: HP1529801T2D_G24


title: HP1529801T2D_D10


title: HP1529801T2D_F5


title: HP1529801T2D_I15


title: HP1529801T2D_D21


title: HP1529801T2D_P5


title: HP1529801T2D_I22


title: HP1529801T2D_P11


title: HP1529801T2D_K16


title: HP1529801T2D_G5


title: HP1529801T2D_L15


title: HP1529801T2D_L24


title: HP1529801T2D_M18


title: HP1529801T2D_C1


title: HP1529801T2D_B23


title: HP1529801T2D_A23


title: HP1529801T2D_D11


title: HP1529801T2D_L14


title: HP1529801T2D_G7


title: HP1529801T2D_F1


title: HP1529801T2D_F11


title: HP1529801T2D_A21


title: HP1529801T2D_O24


title: HP1529801T2D_A15


title: HP1529801T2D_F21


title: HP1529801T2D_F10


title: HP1529801T2D_H20


title: HP1529801T2D_B10


title: HP1529801T2D_J15


title: HP1529801T2D_I13


title: HP1529801T2D_H12


title: HP1529801T2D_F15


title: HP1529801T2D_K19


title: HP1529801T2D_K24


title: HP1529801T2D_D16


title: HP1529801T2D_E16


title: HP1529801T2D_O21


title: HP1529801T2D_B21


title: HP1529801T2D_C12


title: HP1529801T2D_G23


title: HP1529801T2D_M24


title: HP1529801T2D_I18


title: HP1529801T2D_A4


title: HP1529801T2D_K2


title: HP1529801T2D_O15


title: HP1529801T2D_E18


title: HP1529801T2D_P15


title: HP1529801T2D_I2


title: HP1529801T2D_M10


title: HP1529801T2D_G19


title: HP1529801T2D_F2


title: HP1529801T2D_N21


title: HP1529801T2D_I7


title: HP1529801T2D_K3


title: HP1529801T2D_H8


title: HP1529801T2D_B4


title: HP1529801T2D_A7


title: HP1529801T2D_C4


title: HP1529801T2D_H23


title: HP1529801T2D_N10


title: HP1529801T2D_F22


title: HP1529801T2D_H22


title: HP1529801T2D_C23


title: HP1529801T2D_N1


title: HP1529801T2D_L4


title: HP1529801T2D_I24


title: HP1529801T2D_D14


title: HP1529801T2D_B24


title: HP1529801T2D_C13


title: HP1529801T2D_B19


title: HP1529801T2D_I16


title: HP1529801T2D_C2


title: HP1529801T2D_J16


title: HP1529801T2D_F23


title: HP1529801T2D_J4


title: HP1529801T2D_J23


title: HP1529801T2D_P20


title: HP1529801T2D_A13


title: HP1529801T2D_O17


title: HP1529801T2D_D6


title: HP1529801T2D_E3


title: HP1529801T2D_K5


title: HP1529801T2D_E1


title: HP1529801T2D_P22


title: HP1529801T2D_L16


title: HP1529801T2D_O22


title: HP1529801T2D_F20


title: HP1529801T2D_O18


title: HP1529801T2D_C10


title: HP1529801T2D_L22


title: HP1529801T2D_G4


title: HP1529801T2D_I1


title: HP1529801T2D_L1


title: HP1529801T2D_L6


title: HP1529801T2D_O7


title: HP1529801T2D_F16


title: HP1529801T2D_A19


title: HP1529801T2D_D2


title: HP1529801T2D_M22


title: HP1529801T2D_K6


title: HP1529801T2D_K18


title: HP1529801T2D_H15


title: HP1529801T2D_F24


title: HP1529801T2D_B11


title: HP1529801T2D_K23


title: HP1529801T2D_N22


title: HP1529801T2D_O20


title: HP1529801T2D_E24


title: HP1529801T2D_J2


title: HP1529801T2D_H4


title: HP1529801T2D_N4


title: HP1529801T2D_K20


title: HP1529801T2D_O23


title: HP1529801T2D_I17


title: HP1529801T2D_A18


title: HP1529801T2D_M14


title: HP1529801T2D_B2


title: HP1529801T2D_A2


title: HP1529801T2D_F6


title: HP1529801T2D_L9


title: HP1529801T2D_O4


title: HP1529801T2D_N16


title: HP1529801T2D_D9


title: HP1529801T2D_P23


title: HP1529801T2D_M5


title: HP1529801T2D_D17


title: HP1529801T2D_O6


title: HP1529801T2D_D22


title: HP1529801T2D_O2


title: HP1529801T2D_L7


title: HP1529801T2D_C16


title: HP1529801T2D_H17


title: HP1529801T2D_A22


title: HP1529801T2D_I5


title: HP1529801T2D_J17


title: HP1529801T2D_K7


title: HP1529801T2D_K1


title: HP1529801T2D_E5


title: HP1529801T2D_L20


title: HP1529801T2D_J14


title: HP1529801T2D_C11


title: HP1529801T2D_G6


title: HP1529801T2D_N3


title: HP1529801T2D_K13


title: HP1529801T2D_C22


title: HP1529801T2D_C21


title: HP1529801T2D_B3


title: HP1529801T2D_D12


title: HP1529801T2D_H1


title: HP1529801T2D_E15


title: HP1529801T2D_F17


title: HP1529801T2D_N15


title: HP1529801T2D_G9


title: HP1529801T2D_H24


title: HP1529801T2D_F3


title: HP1529801T2D_J18


title: HP1529801T2D_M2


title: HP1529801T2D_G18


title: HP1529801T2D_B5


title: HP1529801T2D_D19


title: HP1529801T2D_N18


title: HP1529801T2D_B9


title: HP1529801T2D_O13


title: HP1529801T2D_B14


title: HP1529801T2D_K17


title: HP1529801T2D_F8


title: HP1529801T2D_J12


title: HP1529801T2D_J11


title: HP1529801T2D_M19


title: HP1529801T2D_M3


title: HP1529801T2D_A9


title: HP1529801T2D_F18


title: HP1529801T2D_B20


title: HP1529801T2D_K21


title: HP1529801T2D_A12


title: HP1529801T2D_C5


title: HP1529801T2D_P3


title: HP1529801T2D_M21


title: HP1529801T2D_P16


title: HP1529801T2D_P9


title: HP1529801T2D_C19


title: HP1529801T2D_A14


title: HP1529801T2D_K22


title: HP1529801T2D_P7


title: HP1529801T2D_L11


title: HP1529801T2D_N14


title: HP1529801T2D_H21


title: HP1529801T2D_H16


title: HP1529801T2D_O19


title: HP1529801T2D_M4


title: HP1529801T2D_J19


title: HP1529801T2D_N23


title: HP1525901_C5

value: Healthy


title: HP1601201T2D_K6


title: HP1601201T2D_C14


title: HP1711701T2D_G6


title: HP1711701T2D_I21


title: HP1525401_F13


title: HP1602301T2D_P21


title: HP1529801T2D_L5


title: HP1525901_L12


title: HP1711701T2D_I19


title: HP1711001_B12


title: HP1602301T2D_D12


title: HP1601201T2D_B6


title: HP1525401_O22


title: HP1529801T2D_L2


title: HP1605601T2D_N7


title: HP1529801T2D_N8


title: HP1525401_J13


title: HP1529801T2D_C7


title: HP1525901_G23


title: HP1601201T2D_K1


title: HP1711701T2D_G8


title: HP1606401T2D_Tn5_F19


title: HP1711701T2D_C15


title: HP1525901_O19


title: HP1711001_F23


title: HP1601201T2D_H1


title: HP1525401_A14


title: HP1601201T2D_C10


title: HP1601201T2D_A5


title: HP1605601T2D_E13


title: HP1605601T2D_M11


title: HP1525401_L2


title: HP1606401T2D_Tn5_J2


title: HP1601201T2D_F8


title: HP1711001_G11


title: HP1602301T2D_A19


title: HP1605601T2D_G18


title: HP1602301T2D_L11


title: HP1711001_I12


title: HP1601201T2D_K9


title: HP1711701T2D_E16


title: HP1605601T2D_E23


title: HP1601201T2D_J2


title: HP1602301T2D_C23


title: HP1711701T2D_K18


title: HP1711001_G4


title: HP1605601T2D_J10


title: HP1714601_C19


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title: HP1602301T2D_J17


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title: HP1606401T2D_Tn5_I17


title: HP1602301T2D_P20


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title: HP1711701T2D_K10


title: HP1602301T2D_O21


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title: HP1711701T2D_P4


title: HP1605601T2D_G13


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title: HP1711701T2D_I11


title: HP1711701T2D_O9


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title: HP1606401T2D_Tn5_N6


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title: HP1602301T2D_H18


title: HP1525901_I11


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title: HP1606401T2D_Tn5_B13


title: HP1711701T2D_D3


title: HP1525901_O14


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title: HP1605601T2D_D11


title: HP1602301T2D_H17


title: HP1601201T2D_D15


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title: HP1605601T2D_A19


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title: HP1606401T2D_Tn5_P6


title: HP1525401_M16


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title: HP1601201T2D_A17


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title: HP1605601T2D_D24


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title: HP1605601T2D_O10


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title: HP1602301T2D_G14


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title: HP1606401T2D_Tn5_M15


title: HP1525401_E18


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title: HP1601201T2D_M22


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title: HP1605601T2D_E10


title: HP1605601T2D_F23


title: HP1525401_M18


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title: HP1525401_F11


title: HP1602301T2D_E23


title: HP1605601T2D_P9


title: HP1602301T2D_E17


title: HP1601201T2D_C5


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title: HP1602301T2D_N17


title: HP1525901_N10


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title: HP1714601_B13


title: HP1711001_N18


title: HP1606401T2D_Tn5_D2


title: HP1605601T2D_B19


title: HP1602301T2D_I8


title: HP1605601T2D_A22


title: HP1525901_F8


title: HP1525401_I10


title: HP1525901_A22


title: HP1714601_A17


title: HP1606401T2D_Tn5_D16


title: HP1601201T2D_A6


title: HP1601201T2D_A11


title: HP1714601_E14


title: HP1602301T2D_F8


title: HP1714601_I23


title: HP1606401T2D_Tn5_K9


title: HP1602301T2D_K19


title: HP1711001_G2


title: HP1711701T2D_I8


title: HP1711701T2D_C13


title: HP1525401_J2


title: HP1606401T2D_Tn5_D17


title: HP1525401_F5


title: HP1601201T2D_D5


title: HP1606401T2D_Tn5_L21


title: HP1601201T2D_J8


title: HP1525901_I2


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title: HP1605601T2D_L13


title: HP1602301T2D_K11


title: HP1525401_J14


title: HP1605601T2D_M17


title: HP1602301T2D_D20


title: HP1525901_E9


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title: HP1525401_H5


title: HP1525401_P5


title: HP1605601T2D_B24


title: HP1605601T2D_J23


title: HP1602301T2D_B22


title: HP1711701T2D_P22


title: HP1605601T2D_I10


title: HP1711701T2D_F5


title: HP1525901_B6


title: HP1601201T2D_E1


title: HP1605601T2D_J12


title: HP1601201T2D_H21


title: HP1714601_B24


title: HP1714601_J7


title: HP1602301T2D_N2


title: HP1606401T2D_Tn5_C5


title: HP1711001_G22


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title: HP1711001_D9


title: HP1605601T2D_C4


title: HP1525901_A19


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title: HP1711701T2D_B7


title: HP1601201T2D_F7


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title: HP1602301T2D_D18


title: HP1711701T2D_F4


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title: HP1605601T2D_C8


title: HP1606401T2D_Tn5_L7


title: HP1525401_O3


title: HP1601201T2D_L18


title: HP1602301T2D_I5


title: HP1606401T2D_Tn5_J7


title: HP1711001_N11


title: HP1711001_J10


title: HP1606401T2D_Tn5_E1


title: HP1602301T2D_L19


title: HP1525401_D5


title: HP1601201T2D_G19


title: HP1601201T2D_L15


title: HP1525901_O21


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title: HP1711001_B8


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title: HP1606401T2D_Tn5_I4


title: HP1606401T2D_Tn5_B2


title: HP1602301T2D_N7


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title: HP1601201T2D_P21


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title: HP1525901_C4


title: HP1605601T2D_D16


title: HP1525901_C21


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title: HP1602301T2D_N10


title: HP1605601T2D_C1


title: HP1601201T2D_L8


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title: HP1714601_N12


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title: HP1602301T2D_L21


title: HP1606401T2D_Tn5_N2


title: HP1711701T2D_M21


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title: HP1601201T2D_L4


title: HP1711701T2D_J23


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title: HP1601201T2D_D13


title: HP1602301T2D_E6


title: HP1601201T2D_M10


title: HP1606401T2D_Tn5_H24


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title: HP1605601T2D_I21


title: HP1606401T2D_Tn5_G9


title: HP1714601_F6


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title: HP1602301T2D_F2


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title: HP1606401T2D_Tn5_N4


title: HP1711701T2D_A17


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title: HP1605601T2D_F13


title: HP1602301T2D_L16


title: HP1605601T2D_B7


title: HP1711701T2D_B21


title: HP1525401_P20


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title: HP1525401_K16


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title: HP1601201T2D_H23


title: HP1601201T2D_O14


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title: HP1711701T2D_M3


title: HP1711001_M11


title: HP1605601T2D_J22


title: HP1714601_C18


title: HP1525901_H3


title: HP1602301T2D_B10


title: HP1601201T2D_H3


title: HP1606401T2D_Tn5_M22


title: HP1602301T2D_L6


title: HP1601201T2D_B8


title: HP1605601T2D_P23


title: HP1606401T2D_Tn5_C9


title: HP1711701T2D_D24


title: HP1525901_P17


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title: HP1605601T2D_H10


title: HP1601201T2D_F20


title: HP1525901_L22


title: HP1602301T2D_B17


title: HP1602301T2D_F5


title: HP1606401T2D_Tn5_H15


title: HP1602301T2D_F24


title: HP1606401T2D_Tn5_J3


title: HP1714601_G14


title: HP1525901_L6


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title: HP1525901_E24


title: HP1525901_N21


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title: HP1606401T2D_Tn5_J1


title: HP1601201T2D_G1


title: HP1602301T2D_O20


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title: HP1606401T2D_Tn5_P11


title: HP1605601T2D_H4


title: HP1605601T2D_H5


title: HP1601201T2D_B14


title: HP1606401T2D_Tn5_E17


title: HP1714601_G2


title: HP1601201T2D_K3


title: HP1714601_F3


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title: HP1605601T2D_G3


title: HP1714601_J21


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title: HP1605601T2D_G6


title: HP1525401_C23


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title: HP1602301T2D_K16


title: HP1602301T2D_B15


title: HP1605601T2D_C9


title: HP1605601T2D_C24


title: HP1602301T2D_O5


title: HP1525901_B10


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title: HP1602301T2D_C4


title: HP1525401_H6


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title: HP1606401T2D_Tn5_N8


title: HP1711701T2D_I13


title: HP1711001_N22


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title: HP1711001_H2


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title: HP1711701T2D_M15


title: HP1711701T2D_C12


title: HP1714601_G18


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title: HP1525901_B15


title: HP1525401_B20


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title: HP1605601T2D_J4


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title: HP1602301T2D_H24


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title: HP1605601T2D_G21


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title: HP1714601_H15


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title: HP1525901_E21


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title: HP1602301T2D_P10


title: HP1602301T2D_O6


title: HP1711001_K15


title: HP1601201T2D_G7


title: HP1605601T2D_D3


title: HP1601201T2D_H15


title: HP1525901_P1


title: HP1602301T2D_F10


title: HP1714601_F1


title: HP1711001_C19


title: HP1601201T2D_P2


title: HP1605601T2D_N21


title: HP1605601T2D_K8


title: HP1601201T2D_J20


title: HP1605601T2D_N19


title: HP1602301T2D_L18


title: HP1525401_I1


title: HP1525401_J7


title: HP1601201T2D_A13


title: HP1711701T2D_K4


title: HP1605601T2D_D9


title: HP1711001_O7


title: HP1714601_I18


title: HP1525401_E7


title: HP1711701T2D_E22


title: HP1602301T2D_C16


title: HP1711701T2D_N10


title: HP1525401_B22


title: HP1525401_O1


title: HP1605601T2D_M3


title: HP1601201T2D_D18


title: HP1602301T2D_C6


title: HP1525401_M12


title: HP1605601T2D_D14


title: HP1711701T2D_M12


title: HP1525901_A14


title: HP1601201T2D_K10


title: HP1525901_C16


title: HP1711001_A15


title: HP1601201T2D_O6


title: HP1606401T2D_Tn5_D10


title: HP1525401_I18


title: HP1714601_E17


title: HP1711701T2D_E17


title: HP1711001_P1


title: HP1602301T2D_M1


title: HP1525901_P13


title: HP1601201T2D_N8


title: HP1714601_K13


title: HP1601201T2D_B7


title: HP1601201T2D_I9


title: HP1605601T2D_P10


title: HP1711001_E17


title: HP1606401T2D_Tn5_I14


title: HP1606401T2D_Tn5_N22


title: HP1711701T2D_G9


title: HP1711001_K5


title: HP1525901_D9


title: HP1601201T2D_H18


title: HP1601201T2D_M23


title: HP1525401_P24


title: HP1605601T2D_I8


title: HP1711701T2D_G17


title: HP1606401T2D_Tn5_J15


title: HP1606401T2D_Tn5_L1


title: HP1711701T2D_F7


title: HP1711001_D4


title: HP1714601_B20


title: HP1605601T2D_B16


title: HP1605601T2D_I12


title: HP1605601T2D_L16


title: HP1601201T2D_E8


title: HP1714601_C10


title: HP1601201T2D_M9


title: HP1605601T2D_A8


title: HP1711001_N15


title: HP1714601_A11


title: HP1525401_D10


title: HP1602301T2D_J24


title: HP1602301T2D_M21


title: HP1601201T2D_O23


title: HP1601201T2D_H7


title: HP1601201T2D_L14


title: HP1525401_D16


title: HP1606401T2D_Tn5_N5


title: HP1606401T2D_Tn5_E4


title: HP1711001_H21


title: HP1525401_G12


title: HP1711701T2D_J16


title: HP1606401T2D_Tn5_F7


title: HP1711701T2D_P8


title: HP1601201T2D_O16


title: HP1711001_F5


title: HP1711701T2D_O12


title: HP1601201T2D_M15


title: HP1605601T2D_M14


title: HP1711701T2D_J11


title: HP1711701T2D_L7


title: HP1525401_A5


title: HP1605601T2D_G15


title: HP1602301T2D_M2


title: HP1525901_M16


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title: HP1711701T2D_N6


title: HP1602301T2D_B13


title: HP1601201T2D_C17


title: HP1605601T2D_L19


title: HP1711001_I16


title: HP1602301T2D_M19


title: HP1711001_L23


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title: HP1601201T2D_E16


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title: HP1714601_N9


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title: HP1525901_I24


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title: HP1711001_M6


title: HP1605601T2D_D2


title: HP1602301T2D_P11


title: HP1525401_G18


title: HP1525901_H7


title: HP1525401_M22


title: HP1711001_O20


title: HP1601201T2D_I1


title: HP1602301T2D_A12


title: HP1605601T2D_B12


title: HP1606401T2D_Tn5_K7


title: HP1711701T2D_I20


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title: HP1711701T2D_J21


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title: HP1605601T2D_L21


title: HP1606401T2D_Tn5_N17


title: HP1602301T2D_O3


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title: HP1602301T2D_P6


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title: HP1711701T2D_C23


title: HP1605601T2D_J7


title: HP1602301T2D_I16


title: HP1606401T2D_Tn5_F13


title: HP1711001_L19


title: HP1601201T2D_J13


title: HP1714601_H13


title: HP1602301T2D_O18


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title: HP1602301T2D_J8


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title: HP1711701T2D_F23


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title: HP1602301T2D_B2


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title: HP1606401T2D_Tn5_C12


title: HP1606401T2D_Tn5_I16


title: HP1711001_D13


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title: HP1606401T2D_Tn5_B4


title: HP1711701T2D_F3


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title: HP1606401T2D_Tn5_J5


title: HP1601201T2D_G6


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title: HP1601201T2D_M8


title: HP1602301T2D_F14


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title: HP1714601_J18


title: HP1605601T2D_C20


title: HP1605601T2D_K11


title: HP1601201T2D_K22


title: HP1525401_J19


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title: HP1601201T2D_A4


title: HP1525901_E7


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title: HP1606401T2D_Tn5_F1


title: HP1525901_I15


title: HP1602301T2D_J6


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title: HP1525901_N15


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title: HP1601201T2D_N13


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title: HP1605601T2D_I24


title: HP1525401_P6


title: HP1602301T2D_K1


title: HP1606401T2D_Tn5_M3


title: HP1711001_M7


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title: HP1711001_K24


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title: HP1605601T2D_O6


title: HP1601201T2D_G3


title: HP1605601T2D_L12


title: HP1711701T2D_N19


title: HP1525401_I3


title: HP1602301T2D_N16


title: HP1525901_B20


title: HP1711001_H12


title: HP1602301T2D_K2


title: HP1711001_L10


title: HP1602301T2D_L7


title: HP1601201T2D_H2


title: HP1605601T2D_D15


title: HP1602301T2D_K22


title: HP1714601_N22


title: HP1605601T2D_J18


title: HP1606401T2D_Tn5_G13


title: HP1606401T2D_Tn5_G20


title: HP1602301T2D_M17


title: HP1605601T2D_H24


title: HP1525901_A8


title: HP1711001_N13


title: HP1525401_I15


title: HP1711701T2D_M20


title: HP1606401T2D_Tn5_L15


title: HP1602301T2D_E2


title: HP1714601_A15


title: HP1606401T2D_Tn5_I15


title: HP1711701T2D_A11


title: HP1711001_C3


title: HP1525901_K18


title: HP1605601T2D_E1


title: HP1602301T2D_J19


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title: HP1525401_N12


title: HP1602301T2D_B21


title: HP1606401T2D_Tn5_K8


title: HP1525901_L23


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title: HP1711701T2D_I3


title: HP1525901_M22


title: HP1601201T2D_O10


title: HP1606401T2D_Tn5_G6


title: HP1714601_O8


title: HP1601201T2D_O19


title: HP1602301T2D_G3


title: HP1602301T2D_L24


title: HP1711001_I21


title: HP1525901_J5


title: HP1605601T2D_I2


title: HP1711001_A21


title: HP1601201T2D_P19


title: HP1714601_J15


title: HP1606401T2D_Tn5_L14


title: HP1606401T2D_Tn5_M21


title: HP1711001_K22


title: HP1711701T2D_D4


title: HP1711701T2D_F9


title: HP1525401_K12


title: HP1525901_B2


title: HP1602301T2D_D23


title: HP1601201T2D_C23


title: HP1525901_O16


title: HP1711701T2D_J15


title: HP1711001_F19


title: HP1525401_D12


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title: HP1711701T2D_G2


title: HP1711001_P10


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title: HP1606401T2D_Tn5_C14


title: HP1606401T2D_Tn5_J14


title: HP1714601_O11


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title: HP1601201T2D_F2


title: HP1711701T2D_E4


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title: HP1601201T2D_A8


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title: HP1601201T2D_K24


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title: HP1605601T2D_E8


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title: HP1711001_M18


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title: HP1606401T2D_Tn5_F5


title: HP1711001_C9


title: HP1714601_H2


title: HP1602301T2D_I23


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title: HP1601201T2D_E13


title: HP1601201T2D_B11


title: HP1525901_J18


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title: HP1525401_M1


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title: HP1525401_B24


title: HP1602301T2D_O11


title: HP1606401T2D_Tn5_E5


title: HP1602301T2D_L22


title: HP1601201T2D_A22


title: HP1605601T2D_B2


title: HP1601201T2D_J19


title: HP1606401T2D_Tn5_F22


title: HP1602301T2D_H5


title: HP1525401_E14


title: HP1601201T2D_C7


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title: HP1606401T2D_Tn5_G1


title: HP1711001_D7


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title: HP1711001_L15


title: HP1606401T2D_Tn5_M6


title: HP1601201T2D_B18


title: HP1606401T2D_Tn5_J21


title: HP1525901_E2


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title: HP1602301T2D_C9


title: HP1711001_A8


title: HP1714601_N18


title: HP1602301T2D_B11


title: HP1606401T2D_Tn5_P18


title: HP1602301T2D_B6


title: HP1606401T2D_Tn5_D6


title: HP1525401_P9


title: HP1525901_A13


title: HP1605601T2D_D21


title: HP1605601T2D_F24


title: HP1711701T2D_F6


title: HP1602301T2D_G16


title: HP1605601T2D_A6


title: HP1711001_K16


title: HP1602301T2D_H16


title: HP1602301T2D_C22


title: HP1601201T2D_J7


title: HP1602301T2D_A21


title: HP1602301T2D_J1


title: HP1601201T2D_A10


title: HP1602301T2D_C7


title: HP1714601_H20


title: HP1601201T2D_P8


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title: HP1711701T2D_D23


title: HP1525401_D15


title: HP1525401_L22


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title: HP1605601T2D_K10


title: HP1714601_B21


title: HP1606401T2D_Tn5_N19


title: HP1714601_G15


title: HP1602301T2D_B9


title: HP1606401T2D_Tn5_C20


title: HP1606401T2D_Tn5_F15


title: HP1601201T2D_O20


title: HP1711701T2D_I12


title: HP1605601T2D_D23


title: HP1714601_P23


title: HP1602301T2D_L20


title: HP1714601_D2


title: HP1601201T2D_N23


title: HP1711701T2D_F11


title: HP1711701T2D_P20


title: HP1525401_N6


title: HP1711001_K7


title: HP1601201T2D_E18


title: HP1711701T2D_A21


title: HP1711701T2D_H10


title: HP1601201T2D_F15


title: HP1601201T2D_C6


title: HP1711701T2D_O7


title: HP1711001_G13


title: HP1711701T2D_F14


title: HP1601201T2D_O7


title: HP1525901_D20


title: HP1525901_D11


title: HP1711001_O1


title: HP1605601T2D_J5


title: HP1602301T2D_L9


title: HP1606401T2D_Tn5_C17


title: HP1714601_L2


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title: HP1602301T2D_M6


title: HP1711001_J22


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title: HP1525901_B13


title: HP1605601T2D_K19


title: HP1601201T2D_D16


title: HP1601201T2D_M6


title: HP1606401T2D_Tn5_I1


title: HP1601201T2D_I3


title: HP1606401T2D_Tn5_G10


title: HP1714601_B22


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title: HP1711701T2D_E13


title: HP1601201T2D_D19


title: HP1601201T2D_O12


title: HP1606401T2D_Tn5_D19


title: HP1606401T2D_Tn5_O1


title: HP1602301T2D_A11


title: HP1605601T2D_N15


title: HP1606401T2D_Tn5_I3


title: HP1525901_E8


title: HP1602301T2D_G8


title: HP1714601_L13


title: HP1602301T2D_G1


title: HP1525901_G11


title: HP1711001_E11


title: HP1525401_P2


title: HP1606401T2D_Tn5_O9


title: HP1711701T2D_G12


title: HP1606401T2D_Tn5_C6


title: HP1525901_H11


title: HP1525901_I14


title: HP1602301T2D_H13


title: HP1525901_D2


title: HP1606401T2D_Tn5_A12


title: HP1605601T2D_H21


title: HP1525901_N22


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title: HP1525901_G24


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title: HP1602301T2D_G21


title: HP1605601T2D_A9


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title: HP1606401T2D_Tn5_N1


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title: HP1605601T2D_P15


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title: HP1602301T2D_C3


title: HP1525401_H7


title: HP1606401T2D_Tn5_B24


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title: HP1711701T2D_C24


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title: HP1711701T2D_I16


title: HP1601201T2D_D17


title: HP1606401T2D_Tn5_A14


title: HP1602301T2D_E1


title: HP1711001_D6


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title: HP1711701T2D_K14


title: HP1714601_B4


title: HP1711001_B11


title: HP1601201T2D_A24


title: HP1525401_K21


title: HP1711701T2D_N2


title: HP1711001_B16


title: HP1606401T2D_Tn5_K2


title: HP1714601_O10


title: HP1605601T2D_C18


title: HP1601201T2D_H24


title: HP1711001_E22


title: HP1714601_H21


title: HP1525401_D4


title: HP1711701T2D_M13


title: HP1711001_L18


title: HP1602301T2D_P4


title: HP1605601T2D_L14


title: HP1602301T2D_P17


title: HP1606401T2D_Tn5_D14


title: HP1711701T2D_E21


title: HP1714601_D24


title: HP1525401_O10


title: HP1525901_O5


title: HP1525901_K13


title: HP1711701T2D_P11


title: HP1525401_A17


title: HP1711701T2D_J24


title: HP1601201T2D_H8


title: HP1605601T2D_P3


title: HP1711001_P22


title: HP1711701T2D_I23


title: HP1602301T2D_G23


title: HP1602301T2D_G4


title: HP1525901_O1


title: HP1606401T2D_Tn5_I8


title: HP1606401T2D_Tn5_C2


title: HP1711001_N20


title: HP1605601T2D_O9


title: HP1606401T2D_Tn5_M12


title: HP1711701T2D_I5


title: HP1602301T2D_I14


title: HP1714601_B12


title: HP1525401_A18


title: HP1711001_H7


title: HP1601201T2D_F13


title: HP1601201T2D_J10


title: HP1605601T2D_O11


title: HP1605601T2D_J24


title: HP1602301T2D_N4


title: HP1525401_J3


title: HP1525901_N6


title: HP1605601T2D_A13


title: HP1525401_I17


title: HP1605601T2D_E17


title: HP1525401_G14


title: HP1525401_H4


title: HP1714601_B9


title: HP1605601T2D_F21


title: HP1525901_E17


title: HP1601201T2D_D10


title: HP1525901_M1


title: HP1714601_G13


title: HP1525901_O3


title: HP1525901_A15


title: HP1711001_K1


title: HP1601201T2D_O5


title: HP1605601T2D_N5


title: HP1602301T2D_I22


title: HP1602301T2D_K24


title: HP1606401T2D_Tn5_A4


title: HP1605601T2D_D12


title: HP1711001_N23


title: HP1714601_K1


title: HP1601201T2D_A3


title: HP1525401_J16


title: HP1714601_G24


title: HP1711001_L11


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title: HP1525901_G2


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title: HP1606401T2D_Tn5_I9


title: HP1606401T2D_Tn5_B11


title: HP1525401_J8


title: HP1601201T2D_F5


title: HP1525401_L9


title: HP1711701T2D_F10


title: HP1602301T2D_I11


title: HP1601201T2D_L9


title: HP1714601_D16


title: HP1711701T2D_H6


title: HP1525401_M4


title: HP1602301T2D_E13


title: HP1711001_J15


title: HP1525401_H3


title: HP1525901_L24


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title: HP1714601_C22


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title: HP1711001_A11


title: HP1711001_M5


title: HP1525901_F1


title: HP1605601T2D_L24


title: HP1711001_B10


title: HP1711701T2D_G4


title: HP1525401_N22


title: HP1525401_P10


title: HP1605601T2D_N9


title: HP1602301T2D_E10


title: HP1602301T2D_B16


title: HP1602301T2D_M16


title: HP1714601_G12


title: HP1605601T2D_O17


title: HP1602301T2D_J7


title: HP1525901_H16


title: HP1605601T2D_B18


title: HP1601201T2D_B3


title: HP1525901_N24


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title: HP1606401T2D_Tn5_K6


title: HP1606401T2D_Tn5_N23


title: HP1601201T2D_E2


title: HP1602301T2D_O15


title: HP1525901_C20


title: HP1601201T2D_B13


title: HP1601201T2D_K13


title: HP1711701T2D_L14


title: HP1606401T2D_Tn5_C4


title: HP1711001_L9


title: HP1711001_F20


title: HP1601201T2D_G24


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title: HP1602301T2D_E4


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title: HP1605601T2D_H14


title: HP1525401_F23


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title: HP1601201T2D_J4


title: HP1605601T2D_A4


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title: HP1602301T2D_B14


title: HP1602301T2D_D8


title: HP1606401T2D_Tn5_H2


title: HP1601201T2D_A1


title: HP1602301T2D_N12


title: HP1606401T2D_Tn5_H12


title: HP1711001_O5


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title: HP1606401T2D_Tn5_L11


title: HP1601201T2D_P15


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title: HP1525901_G3


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title: HP1605601T2D_B10


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title: HP1711001_L14


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title: HP1602301T2D_D24


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title: HP1605601T2D_B14


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title: HP1605601T2D_F10


title: HP1602301T2D_I12


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title: HP1525901_K16


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title: HP1602301T2D_C17


title: HP1602301T2D_C8


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title: HP1525401_H21


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title: HP1606401T2D_Tn5_N24


title: HP1525901_B1


title: HP1714601_B19


title: HP1602301T2D_D2


title: HP1711001_B3


title: HP1606401T2D_Tn5_H1


title: HP1605601T2D_G8


title: HP1606401T2D_Tn5_M1


title: HP1714601_B17


title: HP1525401_E20


title: HP1602301T2D_D16


title: HP1711001_M21


title: HP1711001_D17


title: HP1525401_E9


title: HP1602301T2D_I24


title: HP1525901_I3


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title: HP1714601_O15


title: HP1602301T2D_J14


title: HP1605601T2D_K6


title: HP1601201T2D_G15


title: HP1711001_J21


title: HP1602301T2D_M10


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title: HP1714601_F2


title: HP1711001_F7


title: HP1711701T2D_G10


title: HP1711001_G18


title: HP1605601T2D_M7


title: HP1602301T2D_P18


title: HP1714601_G5


title: HP1601201T2D_N9


title: HP1602301T2D_E19


title: HP1605601T2D_I20


title: HP1711701T2D_F1


title: HP1525901_J19


title: HP1525401_M10


title: HP1525901_E11


title: HP1605601T2D_H17


title: HP1606401T2D_Tn5_D1


title: HP1711001_C16


title: HP1714601_G8


title: HP1711001_P13


title: HP1525901_J24


title: HP1525401_P1


title: HP1605601T2D_B17


title: HP1525401_K7


title: HP1606401T2D_Tn5_G2


title: HP1606401T2D_Tn5_O2


title: HP1711001_P18


title: HP1605601T2D_B13


title: HP1711701T2D_G5


title: HP1525901_C8


title: HP1525901_M18


title: HP1601201T2D_B19


title: HP1525401_A23


title: HP1525901_G22


title: HP1711001_C7


title: HP1525401_L13


title: HP1606401T2D_Tn5_E21


title: HP1601201T2D_H4


title: HP1525401_E17


title: HP1714601_F10


title: HP1602301T2D_A14


title: HP1525901_C17


title: HP1525901_M19


title: HP1606401T2D_Tn5_M8


title: HP1605601T2D_P19


title: HP1711001_I4


title: HP1601201T2D_O4


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title: HP1606401T2D_Tn5_F11


title: HP1602301T2D_N15


title: HP1714601_J17


title: HP1605601T2D_E2


title: HP1525401_E12


title: HP1606401T2D_Tn5_N16


title: HP1711701T2D_N7


title: HP1525901_M6


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title: HP1525901_M4


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title: HP1711701T2D_I22


title: HP1711001_J7


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title: HP1605601T2D_K20


title: HP1714601_D23


title: HP1711001_D2


title: HP1605601T2D_L22


title: HP1605601T2D_H1


title: HP1606401T2D_Tn5_N9


title: HP1525401_J24


title: HP1525401_N13


title: HP1602301T2D_F21


title: HP1525901_P16


title: HP1525901_D5


title: HP1606401T2D_Tn5_H7


title: HP1525901_L19


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title: HP1605601T2D_C19


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title: HP1606401T2D_Tn5_J22


title: HP1606401T2D_Tn5_H5


title: HP1525901_E16


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title: HP1525901_F22


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title: HP1605601T2D_A2


title: HP1525901_H1


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title: HP1711701T2D_N17


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title: HP1602301T2D_I10


title: HP1602301T2D_D9


title: HP1714601_K11


title: HP1711701T2D_G22


title: HP1606401T2D_Tn5_D8


title: HP1605601T2D_K17


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title: HP1525901_H9


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title: HP1606401T2D_Tn5_E8


title: HP1711701T2D_M23


title: HP1711701T2D_B20


title: HP1714601_E22


title: HP1606401T2D_Tn5_L24


title: HP1605601T2D_D7


title: HP1606401T2D_Tn5_O11


title: HP1606401T2D_Tn5_E3


title: HP1601201T2D_C21


title: HP1606401T2D_Tn5_C16


title: HP1525901_L1


title: HP1711701T2D_K8


title: HP1711001_D24


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title: HP1525401_L7


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title: HP1711701T2D_N4


title: HP1602301T2D_F6


title: HP1606401T2D_Tn5_N3


title: HP1525901_B21


title: HP1711701T2D_D8


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title: HP1605601T2D_I16


title: HP1714601_C21


title: HP1714601_D18


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title: HP1602301T2D_J22


title: HP1525401_F8


title: HP1601201T2D_D20


title: HP1606401T2D_Tn5_K1


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title: HP1711701T2D_O5


title: HP1605601T2D_E19


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title: HP1711001_C20


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title: HP1606401T2D_Tn5_L19


title: HP1714601_O24


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title: HP1711001_O2


title: HP1601201T2D_E22


title: HP1525901_D3


title: HP1711701T2D_F8


title: HP1602301T2D_O4


title: HP1525401_B8


title: HP1605601T2D_D10


title: HP1605601T2D_L2


title: HP1714601_B15


title: HP1606401T2D_Tn5_H21


title: HP1602301T2D_K12


title: HP1602301T2D_K23


title: HP1711701T2D_J8


title: HP1606401T2D_Tn5_D20


title: HP1601201T2D_N3


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title: HP1525401_O14


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title: HP1601201T2D_H22


title: HP1525401_G1


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title: HP1606401T2D_Tn5_E14


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title: HP1711701T2D_B12


title: HP1525901_M8


title: HP1525901_H21


title: HP1601201T2D_C15


title: HP1602301T2D_B7


title: HP1714601_I14


title: HP1714601_L10


title: HP1711001_N2


title: HP1601201T2D_M4


title: HP1606401T2D_Tn5_I2


title: HP1525401_L3


title: HP1525401_J4


title: HP1714601_D22


title: HP1601201T2D_E12


title: HP1605601T2D_F17


title: HP1711701T2D_D9


title: HP1714601_F4


title: HP1714601_B10


title: HP1711701T2D_J6


title: HP1525401_L23


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title: HP1602301T2D_E15


title: HP1711701T2D_B8


title: HP1606401T2D_Tn5_E19


title: HP1606401T2D_Tn5_I23


title: HP1605601T2D_O19


title: HP1601201T2D_P24


title: HP1711701T2D_E18


title: HP1606401T2D_Tn5_G12


title: HP1602301T2D_C11


title: HP1714601_K18


title: HP1601201T2D_E20


title: HP1714601_H19


title: HP1711001_C15


title: HP1711001_O22


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title: HP1606401T2D_Tn5_K13


title: HP1711001_P15


title: HP1525401_E8


title: HP1711001_E21


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title: HP1711701T2D_D21


title: HP1602301T2D_P3


title: HP1605601T2D_H12


title: HP1605601T2D_M12


title: HP1605601T2D_A24


title: HP1606401T2D_Tn5_O16


title: HP1525401_E24


title: HP1606401T2D_Tn5_F12


title: HP1605601T2D_K12


title: HP1606401T2D_Tn5_I13


title: HP1711001_N4


title: HP1525401_C4


title: HP1711701T2D_D15


title: HP1711701T2D_J2


title: HP1711701T2D_M9


title: HP1601201T2D_F17


title: HP1605601T2D_O20


title: HP1525901_F5


title: HP1602301T2D_M24


title: HP1601201T2D_N21


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title: HP1525901_D15


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title: HP1601201T2D_N15


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title: HP1711001_H1


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title: HP1711701T2D_E9


title: HP1711001_N17


title: HP1606401T2D_Tn5_O4


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title: HP1601201T2D_O11


title: HP1602301T2D_F19


title: HP1711001_J16


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title: HP1602301T2D_C12


title: HP1605601T2D_E24


title: HP1602301T2D_N3


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title: HP1711701T2D_K3


title: HP1525901_A9


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title: HP1525401_G7


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title: HP1711701T2D_F22


title: HP1714601_H14


title: HP1525401_M20


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title: HP1711701T2D_E24


title: HP1602301T2D_O24


title: HP1714601_E11


title: HP1606401T2D_Tn5_N7


title: HP1525901_M24


title: HP1525401_O20


title: HP1711001_M15


title: HP1525901_B24


title: HP1714601_E2


title: HP1606401T2D_Tn5_E15


title: HP1606401T2D_Tn5_D15


title: HP1602301T2D_I17


title: HP1525401_A7


title: HP1714601_N8


title: HP1711001_A16


title: HP1602301T2D_K9


title: HP1711701T2D_K9


title: HP1714601_I3


title: HP1711701T2D_M4


title: HP1714601_N20


title: HP1525401_P23


title: HP1711701T2D_P9


title: HP1601201T2D_C24


title: HP1711701T2D_O13


title: HP1602301T2D_C13


title: HP1602301T2D_D4


title: HP1602301T2D_E11


title: HP1525901_J7


title: HP1525401_K15


title: HP1606401T2D_Tn5_D3


title: HP1711001_P12


title: HP1711001_M13


title: HP1605601T2D_B9


title: HP1602301T2D_A24


title: HP1602301T2D_G7


title: HP1714601_K7


title: HP1525901_O8


title: HP1602301T2D_B3


title: HP1606401T2D_Tn5_J12


title: HP1605601T2D_B22


title: HP1525401_D8


title: HP1605601T2D_I11


title: HP1711701T2D_K16


title: HP1601201T2D_I15


title: HP1714601_M7


title: HP1714601_A6


title: HP1606401T2D_Tn5_I19


title: HP1602301T2D_N11


title: HP1711001_G10


title: HP1605601T2D_N13


title: HP1601201T2D_O15


title: HP1525401_F14


title: HP1711001_G7


title: HP1605601T2D_K9


title: HP1605601T2D_F15


title: HP1525901_N14


title: HP1601201T2D_K23


title: HP1605601T2D_A10


title: HP1601201T2D_A2


title: HP1602301T2D_K6


title: HP1525901_G19


title: HP1605601T2D_D22


title: HP1601201T2D_L11


title: HP1601201T2D_O21


title: HP1606401T2D_Tn5_D11


title: HP1601201T2D_K14


title: HP1714601_D13


title: HP1605601T2D_E5


title: HP1525901_O13


title: HP1605601T2D_H18


title: HP1606401T2D_Tn5_H4


title: HP1605601T2D_F2


title: HP1711701T2D_I6


title: HP1711701T2D_J22


title: HP1525401_P7


title: HP1605601T2D_M21


title: HP1601201T2D_L2


title: HP1601201T2D_O18


title: HP1711701T2D_C19


title: HP1602301T2D_L12


title: HP1711701T2D_D17


title: HP1714601_E23


title: HP1601201T2D_G13


title: HP1602301T2D_K15


title: HP1605601T2D_I1


title: HP1606401T2D_Tn5_E7


title: HP1714601_C17


title: HP1525901_D21


title: HP1525901_E14


title: HP1525401_G16


title: HP1711001_I1


title: HP1605601T2D_P22


title: HP1525901_M2


title: HP1711701T2D_G20


title: HP1525401_I24


title: HP1602301T2D_K4


title: HP1525401_M2


title: HP1525901_H20


title: HP1606401T2D_Tn5_C13


title: HP1525401_K23


title: HP1602301T2D_O1


title: HP1714601_I10


title: HP1602301T2D_M8


title: HP1711001_I17


title: HP1711701T2D_C4


title: HP1602301T2D_D3


title: HP1714601_J20


title: HP1606401T2D_Tn5_H17


title: HP1711001_E15


title: HP1525901_I6


title: HP1525401_K2


title: HP1605601T2D_E9


title: HP1605601T2D_M22


title: HP1601201T2D_D9


title: HP1711001_E4


title: HP1601201T2D_P4


title: HP1606401T2D_Tn5_D5


title: HP1711001_M4


title: HP1602301T2D_J4


title: HP1605601T2D_N4


title: HP1711701T2D_H23


title: HP1711001_F1


title: HP1711701T2D_O19


title: HP1602301T2D_F23


title: HP1711001_O23


title: HP1711001_O9


title: HP1601201T2D_H20


title: HP1525401_P17


title: HP1602301T2D_B5


title: HP1525401_B16


title: HP1601201T2D_K20


title: HP1601201T2D_L17


title: HP1525401_F17


title: HP1714601_F14


title: HP1602301T2D_M22


title: HP1525401_B19


title: HP1711701T2D_P14


title: HP1525401_M6


title: HP1605601T2D_J14


title: HP1605601T2D_P6


title: HP1606401T2D_Tn5_B3


title: HP1605601T2D_M2


title: HP1602301T2D_O8


title: HP1714601_M5


title: HP1525901_F20


title: HP1714601_D3


title: HP1605601T2D_A3


title: HP1711001_N7


title: HP1602301T2D_E16


title: HP1525901_F14


title: HP1525401_M11


title: HP1602301T2D_A1


title: HP1525401_J22


title: HP1602301T2D_P23


title: HP1605601T2D_N8


title: HP1605601T2D_M24


title: HP1606401T2D_Tn5_P20


title: HP1605601T2D_L18


title: HP1525901_P2


title: HP1525401_P18


title: HP1525901_E4


title: HP1525901_P19


title: HP1711701T2D_B10


title: HP1714601_A23


title: HP1711701T2D_A9


title: HP1711001_O17


title: HP1525901_O18


title: HP1601201T2D_H19


title: HP1605601T2D_J3


title: HP1606401T2D_Tn5_G11


title: HP1525401_K20


title: HP1606401T2D_Tn5_P1


title: HP1602301T2D_B18


title: HP1525401_L21


title: HP1601201T2D_L24


title: HP1602301T2D_A9


title: HP1602301T2D_L23


title: HP1525401_P11


title: HP1714601_H16


title: HP1605601T2D_O5


title: HP1601201T2D_N20


title: HP1602301T2D_C21


title: HP1711001_M17


title: HP1711001_E19


title: HP1714601_N17


title: HP1714601_M1


title: HP1525401_E10


title: HP1605601T2D_A18


title: HP1525401_F15


title: HP1601201T2D_C22


title: HP1711001_P2


title: HP1714601_A12


title: HP1602301T2D_D17


title: HP1605601T2D_A12


title: HP1714601_B2


title: HP1711001_K10


title: HP1525901_B9


title: HP1602301T2D_H22


title: HP1606401T2D_Tn5_P8


title: HP1714601_B8


title: HP1605601T2D_G17


title: HP1605601T2D_P5


title: HP1711701T2D_I1


title: HP1601201T2D_D22


title: HP1525401_L4


title: HP1525901_H18


title: HP1714601_J14


title: HP1602301T2D_P9


title: HP1711001_F17


title: HP1525401_N19


title: HP1525901_M14


title: HP1711001_E20


title: HP1525401_H19


title: HP1711001_K18


title: HP1606401T2D_Tn5_A7


title: HP1601201T2D_I10


title: HP1602301T2D_N5


title: HP1601201T2D_C9


title: HP1602301T2D_K14


title: HP1525401_A19


title: HP1711001_A22


title: HP1602301T2D_I4


title: HP1606401T2D_Tn5_L5


title: HP1602301T2D_D10


title: HP1602301T2D_M11


title: HP1605601T2D_P8


title: HP1525901_H4


title: HP1714601_O17


title: HP1711701T2D_O2


title: HP1602301T2D_C24


title: HP1711701T2D_H4


title: HP1602301T2D_I13


title: HP1602301T2D_I7


title: HP1602301T2D_D5


title: HP1525901_L15


title: HP1711001_I8


title: HP1714601_M19


title: HP1601201T2D_L3


title: HP1602301T2D_H8


title: HP1525901_K14


title: HP1601201T2D_I14


title: HP1602301T2D_E8


title: HP1525901_B7


title: HP1605601T2D_I14


title: HP1601201T2D_P14


title: HP1525401_L19


title: HP1711001_I13


title: HP1605601T2D_I6


title: HP1525901_O20


title: HP1601201T2D_F1


title: HP1602301T2D_L4


title: HP1711001_C18


title: HP1605601T2D_O15


title: HP1711001_F11


title: HP1601201T2D_B2


title: HP1605601T2D_K22


title: HP1602301T2D_F22


title: HP1525401_K22


title: HP1601201T2D_C12


title: HP1602301T2D_H3


title: HP1714601_E24


title: HP1605601T2D_P18


title: HP1711001_I7


title: HP1711701T2D_J9


title: HP1525901_F11


title: HP1601201T2D_C3


title: HP1605601T2D_C3


title: HP1606401T2D_Tn5_F6


title: HP1605601T2D_F11


title: HP1714601_G6


title: HP1602301T2D_O13


title: HP1602301T2D_C20


title: HP1714601_M13


title: HP1606401T2D_Tn5_O8


title: HP1602301T2D_L14


title: HP1714601_F11


title: HP1525901_L16


title: HP1711001_J9


title: HP1601201T2D_D14


title: HP1601201T2D_A12


title: HP1525401_C17


title: HP1601201T2D_E6


title: HP1525901_H17


title: HP1606401T2D_Tn5_C19


title: HP1601201T2D_G9


title: HP1711001_N21


title: HP1714601_E18


title: HP1711701T2D_D12


title: HP1605601T2D_P14


title: HP1714601_E10


title: HP1605601T2D_L6


title: HP1525901_G14


title: HP1711001_J17


title: HP1601201T2D_A16


title: HP1711001_H16


title: HP1525401_E22


title: HP1606401T2D_Tn5_I21


title: HP1602301T2D_M18


title: HSCT#3_postHSCT_blood

first: Dan

last: Sun

department: MedH

description: HSCT #3 donor blood

data_processing:
Raw sequencing data in fastq format was combined from all runs and demultiplexed into the individual 10x Genomics runs using deML v1.1.3 allowing up to 2 mismatches. Next, single-cell data was processed using zUMIs v2.9.7. Within zUMIs, we applied clipping of poly-A tails, cell barcode detection and error correction of cell barcodes and UMIs. Reads were mapped to the human genome (GRCh38) and gene expression quantified using Gencode v35 annotations. All gene counts including those derived from empty droplets were exported into sparse matrices from zUMIs. We then used CellBender 0.1.0 to remove ambient RNA background signal and define those droplets containing real cells. Doublets were removed using solo 1.0.
Aligned and tagged reads from zUMIs in bam format were combined from all samples. We tabulated the per-cell coverage over 7,416,067 SNP positions (most common SNPs with an allele frequency surpassing 5% derived from the 1000 Genomes Project phase 3 release) for all retained cells (see above) using cellSNP-lite 1.2.0. Next, cells were sorted into a range of five to 10 genetic identities (--nDonor) using Vireo 0.4.2. Among these, eight was chosen as the optimal count given it represented the lowest number of identities while concurrently exhibiting the minimal number of genetic doublets. Cells with failed identity inference (“unassigned”) or mixed genotypes (“doublet”) were discarded.
The expression matrices from the each sample were log-normalized, and the normalized expression data of the top 2000 most variable features (selection.method = ‘vst’) were scaled, and PCA dimensionality reduction was subsequently performed with npcs = 30 in Seurat 4.3. To integrate expression data from different samples, reciprocal PCA (RPCA) was employed with a configuration of k.anchor = 20, applied separately to blood and tissue samples. Neighborhood graph and uniform manifold approximation and projection (UMAP) and clustering were then performed on the integrated assay in Seurat.
Assembly: hg38
Supplementary files format and content: *_soloed.h5ad: zUMI, CellBender and solo processed expression data per sample
Supplementary files format and content: tissue_metadata.csv: sample info, cell type, and inferred cell origin (donor/recipient) per cell for tissue samples
Supplementary files format and content: tissue_barcodes.tsv.gz: list of barcodes for tissue samples
Supplementary files format and content: tissue_features.tsv.gz: list of genes for tissue samples
Supplementary files format and content: tissue_matrix.mtx.gz: gene expression counts for tissue samples in Matrix Market Exchange format
Supplementary files format and content: tissue_umap.csv: umap coordinates for tissue samples
Supplementary files format and content: donor_blood_metadata.csv: sample info per cell for donor blood samples
Supplementary files format and content: donor_blood_barcodes.tsv.gz: list of barcodes for donor blood samples
Supplementary files format and content: donor_blood_features.tsv.gz: list of genes for donor blood samples
Supplementary files format and content: donor_blood_matrix.mtx.gz: gene expression counts for donor blood samples in Matrix Market Exchange format

source_name: peripheral blood

extract_protocol:
For the first UTX sample (UTX#1), targeted Fluorescence-activated single cell (FACS) sorting was used to obtain leukocyte subsets (B cells from donor peripheral blood, monocytes from recipient peripheral blood, T and NK cells from recipient tissue). Alive CD45+ sorted mononuclear cells were obtained from the remaining UTX and HSCT samples. All samples were then processed with the 10x Genomics single cell gene expression kit according to manufacturer's instructions to obtain gene expression libraries.
10x Genomics Gene Expression libraries were converted to single-stranded circular DNA from 50 ng using the Universal Library Conversion Kit (App-A; MGI Tech) according to the manufacturer’s instructions. Libraries were pooled and 60 fmol of the pool was used to generate DNA nanoballs directly prior to sequencing on two FCL flow cells on the DNBSEQ G400RS platform (MGI Tech).

value: peripheral blood

tag: Sex

value: female


title: HP1711001_N1


title: HSCT#4_postHSCT_blood

description: HSCT #4 donor blood

value: male


title: HP1711701T2D_M16


title: HP1525401_M3


title: HP1602301T2D_D11


title: HP1525401_F7


title: HSCT#4_postHSCT_tissue

description: HSCT #4 recipient tissue

source_name: menstrual blood

value: menstrual blood


title: HP1602301T2D_G15


title: HP1711001_A1


title: HSCT#3_postHSCT_tissue

description: HSCT #3 recipient tissue


title: UTX#3_recipient_tissue

description: UTX #3 recipient tissue

source_name: endometrium

value: endometrium


title: HP1602301T2D_B1


title: HP1525401_O9


title: HP1602301T2D_D13


title: UTX#2_donor_blood

description: UTX #2 donor blood


title: UTX#2_recipient_tissue

description: UTX #2 recipient tissue


title: HP1525401_L12


title: HP1601201T2D_I16


title: HP1606401T2D_Tn5_G5


title: UTX#1_donor_recipient_combined

description: UTX #1 B cells (donor blood), monocytes (recipient blood), T and NK cells (recipient tissue)

source_name: peripheral blood + endometrium

value: peripheral blood + endometrium

value: Mixed (see description)


title: UTX#3_donor_blood

description: UTX #3 donor blood


title: HP1525401_B12


title: HP1605601T2D_C16


title: HP1602301T2D_P1


title: mouse-Veh-Hdac2KO-5

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Sequencing adapters were removed using Trimmomatic v.0.33
Reads were aligned to the mouse genome (autosomes, mitochondrial and sex chromosomes only)  using the subread v.1.6.2 aligner
Gene counts were obtained for each sample based on the GRCm38 Ensembl transcriptome (v.87) using the featureCounts v.1.2.6 software
Assembly: GRCm38
Supplementary files format and content: featureCounts output files

organism: Mus musculus

source_name: bilateral front cortex

extract_protocol:
Qiagen™ RNeasy mini kit
RiboMinus™ Human/Mouse Transcriptome

treatment_protocol: E6R was dissolved in a vehicle solution containing saline 55% v/v, DMSO 34% v/v, ethanol 5% v/v, kolliphor EL (Sigma-Aldrich) 5% v/v, and NaOH 1M 1% v/v. The vehicle group received the same solution without E6R. The number of mice per group was: WT+vehicle (n = 5), WT+50 mg/kg E6R (n = 5), Hdac2 cKO+vehicle (n = 6) and Hdac2 cKO+50 mg/kg E6R (n = 6). Animals were injected daily by intraperitoneal injection with 5 μL/g of the solution (50 mg/kg of E6R, or vehicle) at 11 AM for 10 days. Animal wellness was verified by daily visual inspection and weighing. No abnormal behaviour or significant body mass decrease (>5%) was noted in all groups. On day 11, animals were sacrificed by bleeding via heart puncture under carbon dioxide anesthesia. The brains were quickly removed and the bilateral frontal cortex (bregma 1.90 to 1.40 mm) was dissected followed by total RNA extraction.

value: bilateral front cortex

value: Hdac2 cKO in pyramidal neurons

value: Vehicle (saline 55% v/v, DMSO 34% v/v, ethanol 5% v/v, kolliphor EL (Sigma-Aldrich) 5% v/v, and NaOH 1M 1% v/v)


title: HP1711001_A4


title: mouse-Veh-WT-4

value: wild-type


title: mouse-Veh-WT-3


title: mouse-Veh-WT-2


title: HP1525901_G1


title: HP1714601_A20


title: mouse-Veh-WT-1


title: HP1714601_E3


title: HP1711701T2D_C18


title: mouse-Veh-Hdac2KO-3


title: mouse-Veh-WT-5


title: HP1606401T2D_Tn5_C10


title: HP1711701T2D_M7


title: mouse-Veh-Hdac2KO-4


title: mouse-Veh-Hdac2KO-1


title: HP1605601T2D_O3


title: mouse-E6R-WT-5

value: 50 mg/kg E6R (in saline 55% v/v, DMSO 34% v/v, ethanol 5% v/v, kolliphor EL (Sigma-Aldrich) 5% v/v, and NaOH 1M 1% v/v)


title: HP1711001_E13


title: HP1714601_N24


title: mouse-Veh-Hdac2KO-2


title: HP1602301T2D_A16


title: mouse-E6R-WT-4


title: HP1714601_M24


title: mouse-Veh-Hdac2KO-6


title: mouse-E6R-WT-3


title: mouse-E6R-WT-2


title: HP1606401T2D_Tn5_L8


title: HP1602301T2D_D6


title: mouse-E6R-WT-1


title: HP1605601T2D_G12


title: mouse-E6R-Hdac2KO-4


title: mouse-E6R-Hdac2KO-6


title: HP1525401_I13


title: HP1525401_A24


title: mouse-E6R-Hdac2KO-1


title: mouse-E6R-Hdac2KO-5


title: HP1601201T2D_M14


title: HP1605601T2D_N3


title: HP1606401T2D_Tn5_I22


title: HP1602301T2D_L8


title: HP1714601_L20


title: mouse-E6R-Hdac2KO-3


title: DNA from Congenital biliary dilatation patient-27

type: genomic

city: Shenzhen

first: feng

last: qi

address: No.7019 Yitian Road, Futian District

country: China

institute: Shen zhen Children’s Hospital

hyb_protocol: Bisulphite converted DNA was amplified,fragmented and hybridized to human infinium Methylation EPIC BeadChip(illumina) using standard illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader(Hiscan)and standard recommended illumina scanner setting

data_processing: RnBeads package in R package(v4.1.1)

label: Cy3, Cy5

molecule: genomic DNA

source_name: peripheral blood DNA frpm Congenital biliary dilatation patients

label_protocol: Standard illumina protocol

extract_protocol: DNA from whole blood of patients and controls was meticulously extracted using a reagent kit sourced from YEASEN (China), in strict compliance with the manufacturer's protocol.

value: congenital biliary dilatation


title: HP1711701T2D_N18

value: Pancreatic islets


title: DNA from healthy control 40

source_name: DNA from healthy control

value: healthy control


title: HP1606401T2D_Tn5_M5


title: DNA from healthy control 5


title: HP1602301T2D_G19


title: DNA from Congenital biliary dilatation patient-94


title: DNA from Congenital biliary dilatation patient-91


title: HP1711001_B19


title: HP1711701T2D_G15


title: DNA from healthy control 37


title: HP1714601_A22


title: DNA from Congenital biliary dilatation patient-87


title: HP1711001_G12


title: DNA from Congenital biliary dilatation patient-86


title: DNA from healthy control 34


title: DNA from Congenital biliary dilatation patient-82


title: HP1601201T2D_G12


title: HP1606401T2D_Tn5_L9


title: mouse-E6R-Hdac2KO-2


title: DNA from healthy control 33


title: HP1605601T2D_K18


title: DNA from healthy control 39


title: DNA from Congenital biliary dilatation patient-79


title: HP1605601T2D_A7


title: HP1711701T2D_H18


title: DNA from healthy control 32


title: DNA from Congenital biliary dilatation patient-77


title: HP1711701T2D_B13


title: DNA from Congenital biliary dilatation patient-74


title: DNA from healthy control 29


title: HP1602301T2D_C10


title: DNA from Congenital biliary dilatation patient-70


title: HP1525901_I20


title: HP1711001_A2


title: DNA from healthy control 28


title: HP1711701T2D_N22


title: HP1606401T2D_Tn5_A2


title: DNA from healthy control 27


title: HP1605601T2D_I5


title: DNA from Congenital biliary dilatation patient-64


title: DNA from healthy control 24


title: DNA from Congenital biliary dilatation patient-65


title: DNA from Congenital biliary dilatation patient-73


title: DNA from healthy control 23


title: HP1711701T2D_D7


title: HP1602301T2D_I20


title: HP1605601T2D_B4


title: DNA from Congenital biliary dilatation patient-107


title: HP1711701T2D_E6


title: DNA from Congenital biliary dilatation patient-62


title: HP1601201T2D_P17


title: HP1714601_H22


title: DNA from Congenital biliary dilatation patient-57


title: HP1606401T2D_Tn5_A8


title: DNA from Congenital biliary dilatation patient-52


title: HP1711701T2D_H21


title: HP1602301T2D_P5


title: HP1711701T2D_G7


title: HP1605601T2D_H20


title: DNA from Congenital biliary dilatation patient-56


title: HP1711001_F6


title: DNA from Congenital biliary dilatation patient-51


title: DNA from healthy control 22


title: DNA from healthy control 16


title: DNA from Congenital biliary dilatation patient-48


title: HP1525901_K17


title: DNA from healthy control 20


title: HP1606401T2D_Tn5_P4


title: DNA from Congenital biliary dilatation patient-105


title: HP1606401T2D_Tn5_P2


title: HP1606401T2D_Tn5_E22


title: DNA from Congenital biliary dilatation patient-35


title: DNA from healthy control 19


title: DNA from Congenital biliary dilatation patient-67


title: DNA from healthy control 18


title: HP1601201T2D_J5


title: HP1714601_D21


title: HP1525901_K11


title: HP1714601_H4


title: DNA from healthy control 15


title: HP1601201T2D_M5


title: HP1606401T2D_Tn5_G17


title: HP1602301T2D_C5


title: DNA from Congenital biliary dilatation patient-28


title: HP1711701T2D_A8


title: HP1601201T2D_K18


title: DNA from healthy control 9


title: HP1525401_K9


title: DNA from Congenital biliary dilatation patient-104


title: DNA from Congenital biliary dilatation patient-21


title: HP1605601T2D_O21


title: DNA from healthy control 12


title: HP1601201T2D_O8


title: DNA from Congenital biliary dilatation patient-33


title: HP1601201T2D_I21


title: DNA from Congenital biliary dilatation patient-19


title: HP1601201T2D_B23


title: DNA from Congenital biliary dilatation patient-30


title: HP1711701T2D_P19


title: DNA from healthy control 10


title: HP1525401_D20


title: DNA from Congenital biliary dilatation patient-108


title: DNA from healthy control 6


title: HP1602301T2D_A13


title: DNA from Congenital biliary dilatation patient-99


title: HP1711701T2D_H1


title: HP1711701T2D_I10


title: HP1714601_M17


title: HP1714601_L22


title: Primary_9, Primary_11, Primary_12, scRNAseq  HTO

city: Portland

first: FURKAN

last: OZMEN

state: OR

address: 2720 S Moody Ave, Portland, OR 97201,USA

department: Division of Oncological Sciences

institute: Oregon Health & Science University

description:
Library name: Sample9_Sample11_Sample12_HTO
10x Genomics

data_processing:
Raw sequencing data were aligned to GRCh38 genome reference using 10X software CellRanger (Version 6.1.2) with default parameters. For multiplexed samples additional demultiplexing step was added.
Assembly: hg38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Breast

extract_protocol:
Tumor tissues were disaggregated by gentleMACS kits (Miltenyi Biotec, #130-095-929) following the manufactural instructions. The lysate was resuspended and filtered through a 70-µm cell strainer (130-098-462; Miltenyi Biotec Germany). Cells were collected by centrifuging (300 × g for 7 min at 4 °C) and resuspended at 700–1200 cells/µl. Live cells were isolated by EasySep Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, #17899).
Single cell suspensions were processed according to 10xGenomics scRNAseq sample preparation protocol (Chromium Next GEM Single Cell 3' Kit v3.1, 10xGenomics). The entire mixed cell population was further analyzed without sorting or enrichment for specific cell subtypes. Cell suspensions were uploaded into the Chromium controller, capturing GEMs that encapsulated an estimated 5,000-10,000 single cells per channel. Library construction was sequenced on the NovaSeq 6000. All steps were performed according to the manufacturer’s standard protocol.

value: Breast

tag: tissue type

value: primary

value: Dissociated cells from breast cancer patient biopsy


title: DNA from Congenital biliary dilatation patient-14

value: peripheral blood


title: Primary_8, Primary_10, scRNAseq HTO

description:
Library name: Sample8_Sample10_HTO
10x Genomics


title: DNA from healthy control 11


title: HP1711701T2D_O22


title: HP1606401T2D_Tn5_I6


title: DNA from Congenital biliary dilatation patient-9


title: DNA from Congenital biliary dilatation patient-29


title: HP1606401T2D_Tn5_D13


title: DNA from Congenital biliary dilatation patient-7


title: Primary_2, Metastasis_3, scRNAseq HTO

description:
Library name: Sample2_Sample15_HTO
10x Genomics

value: primary, Metastasis


title: Primary_2, Metastasis_3, scRNAseq

description:
Library name: Sample2_Sample15
10x Genomics


title: HP1714601_I1

value: Healthy


title: DNA from healthy control 1


title: Primary_9, Primary_11, Primary_12, scRNAseq

description:
Library name: Sample9_Sample11_Sample12
10x Genomics


title: Metastasis_9, scRNAseq

description:
Library name: Sample21
10x Genomics

source_name: Bone

value: Bone

value: Metastasis


title: DNA from Congenital biliary dilatation patient-1


title: HP1711701T2D_J7


title: HP1605601T2D_F12


title: HP1711001_E5


title: HP1525401_O18


title: Primary_8, Primary_10, scRNAseq

description:
Library name: Sample8_Sample10
10x Genomics


title: DNA from Congenital biliary dilatation patient-5


title: HP1525901_M10


title: HP1714601_C11


title: Metastasis_11, scRNAseq

description:
Library name: Sample23
10x Genomics

source_name: Liver

value: Liver


title: Metastasis_6, scRNAseq

description:
Library name: Sample18
10x Genomics

source_name: Lymph Node

value: Lymph Node


title: HP1525901_M12


title: Metastasis_4, scRNAseq

description:
Library name: Sample16
10x Genomics


title: HP1711001_H5


title: HP1711701T2D_C9


title: HP1605601T2D_P24


title: Metastasis_2, scRNAseq

description:
Library name: Sample14
10x Genomics

source_name: Mediastinum

value: Mediastinum


title: HP1711701T2D_H19


title: HP1525401_H11


title: Metastasis_10, scRNAseq

description:
Library name: Sample22
10x Genomics


title: HP1605601T2D_L1


title: Metastasis_8, scRNAseq

description:
Library name: Sample20
10x Genomics

source_name: Adrenal Gland

value: Adrenal Gland


title: HP1714601_D19


title: HP1525901_B17


title: HP1711701T2D_B24


title: Primary_5, scRNAseq

description:
Library name: Sample5
10x Genomics


title: Primary_3, scRNAseq

description:
Library name: Sample3
10x Genomics


title: Metastasis_5, scRNAseq

description:
Library name: Sample17
10x Genomics


title: Primary_1, scRNAseq

description:
Library name: Sample1
10x Genomics


title: HP1525401_J17


title: HP1525401_G3


title: HP1525401_O17


title: SCC-15 cells, shTTK, rep1

city: Xi'an

first: Tianjie

last: Liu

state: Shannxi

address: No.277, Yanta West Road

institute: The First Affiliated Hospital of Xi'an Jiaotong University

description: Library name: SCC_15_shTTK_rep1

data_processing:
Raw reads were processed using trim-galore (0.6.6).  Low quality reads were removed to obtain the clean reads. The clean reads were mapped to reference genome using STAR (2.7.7a).
Raw read counts of each gene were obtained by featureCounts (2.0.1).
Supplementary files format and content: tab-delimited text files include count values for each Sample.
Assembly: hg38
Supplementary files format and content: Raw_counts

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA quantity and integrity were assessed by Qubit and Agilent Bioanalyzer.
Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, and converted to cDNA. Strand specificity was achieved via dUTP incorporation during second-strand synthesis. After end repair/A-tailing, indexed adapters were ligated, libraries were PCR-amplified, QC’d (Bioanalyzer/Fragment Analyzer), pooled, and Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument.

value: Oral squamous cell carcinoma cells

value: TTK knockdown

value: Untreated


title: Primary_6, scRNAseq

description:
Library name: Sample6
10x Genomics


title: Primary_7, scRNAseq

description:
Library name: Sample7
10x Genomics


title: Metastasis_7, scRNAseq

description:
Library name: Sample19
10x Genomics


title: SCC-15cells, shTTK, rep3

description: Library name: SCC_15_shTTK_rep3


title: HP1711001_C12

value: Pancreatic islets


title: HP1714601_O1


title: SCC-15 cells, shControl, rep3

description: Library name: SCC_15_shControl_rep3

value: WT


title: Primary_4, scRNAseq

description:
Library name: Sample4
10x Genomics

value: Breast


title: SCC-15 cells, shControl, rep2

description: Library name: SCC_15_shControl_rep2


title: HP1525401_A20


title: HP1601201T2D_I18


title: HP1525901_J12


title: HP1605601T2D_H19


title: HP1525901_N2


title: CAL-27 cells, shTTK, rep3

description: Library name: CAL_27_shTTK_rep3


title: HP1601201T2D_I22


title: HP1602301T2D_A10


title: Metastasis_1, scRNAseq

description:
Library name: Sample13
10x Genomics


title: SCC-15 cells, shControl, rep1

description: Library name: SCC_15_shControl_rep1


title: CAL-27 cells, shTTK, rep2

description: Library name: CAL_27_shTTK_rep2


title: CAL-27 cells, shControl, rep3

description: Library name: CAL_27_shControl_rep3


title: HP1601201T2D_A14


title: HP1605601T2D_I19


title: CAL-27 cells, shTTK, rep1

description: Library name: CAL_27_shTTK_rep1


title: HP1602301T2D_I1


title: CAL-27 cells, shControl, rep2

description: Library name: CAL_27_shControl_rep2


title: SCC-15 cells, shTTK, rep2

description: Library name: SCC_15_shTTK_rep2


title: HP1605601T2D_F4


title: CAL-27 cells, shControl, rep1

description: Library name: CAL_27_shControl_rep1


title: HP1606401T2D_Tn5_P15


title: HP1605601T2D_N6


title: 2705-XX-98

city: San Diego

first: Kellen

last: Cavagnero

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

description: Library name: 2705-XX-98

data_processing:
Reads were mapped to the GRCh38 reference genome using STAR. Count matrices were generated using HTSeq. Differential expression analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: count matrix

source_name: skin

extract_protocol:
Samples were incubated in an optimized lysis buffer, which contains proteinase K, to release RNA from the sample sections. This was followed by an incubation at a higher temperature to partially reverse formalin crosslinking of the released nucleic acids and improve RNA yield and quality. This was followed by DNase treatment that was optimized to eliminate all genomic DNA, including very small DNA fragments. The lysate was then mixed with Buffer RBC, and ethanol was added to provide appropriate binding conditions for RNA. The sample was then applied to an RNeasy MinElute spin column, where the total RNA bound to the membrane and contaminants were effectively washed away. RNA was then eluted in 30µl of RNase-free water.
Libraries were generated using NovaSeq.

value: skin

value: skin cells


title: 7798-JF

description: Library name: 7798-JF

data_processing:
Reads were mapped to the GRCh38 reference genome and count matrices were generated using CellRanger with default parameters. Downstream processing, and analysis was done using Seurat.
Assembly: hg38
Supplementary files format and content: count matrix

molecule: nuclear RNA

extract_protocol:
Samples were incubated in an optimized lysis buffer, which contains proteinase K, to release RNA from the sample sections. This was followed by an incubation at a higher temperature to partially reverse formalin crosslinking of the released nucleic acids and improve RNA yield and quality. This was followed by DNase treatment that was optimized to eliminate all genomic DNA, including very small DNA fragments. The lysate was then mixed with Buffer RBC, and ethanol was added to provide appropriate binding conditions for RNA. The sample was then applied to an RNeasy MinElute spin column, where the total RNA bound to the membrane and contaminants were effectively washed away. RNA was then eluted in 30µl of RNase-free water.
10X Genomics Flex FFPE protocol and were subjected to 28x91bp of sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan


title: HP1711001_F21


title: 2705-XX-99

description: Library name: 2705-XX-99


title: HP1605601T2D_F14


title: HP1605601T2D_I9


title: HP1605601T2D_G22


title: 2705-XX-97

description: Library name: 2705-XX-97


title: HP1711001_H10


title: 2705-XX-96

description: Library name: 2705-XX-96


title: 2705-XX-95

description: Library name: 2705-XX-95


title: 2705-XX-94

description: Library name: 2705-XX-94


title: HP1525401_I2


title: 2705-XX-93

description: Library name: 2705-XX-93


title: HP1711001_J6


title: HP1714601_A21


title: 2705-XX-92

description: Library name: 2705-XX-92


title: 2705-XX-91

description: Library name: 2705-XX-91


title: 2705-XX-90

description: Library name: 2705-XX-90


title: HP1711701T2D_F24


title: HP1525901_K12


title: HP1606401T2D_Tn5_C11


title: HP1525901_J2


title: HP1605601T2D_L17