title: HCT116 AsiSI KD_input

city: Beijing

first: Jianfeng

last: Fu

address: Yiheyuan Road

institute: Peking university

data_processing:
the quality of each raw sequencing file (fastq) was verified with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
All files were aligned to the reference human genome (hg19) and processed using bowtie2 (https://bowtie-bio.sourceforge.net/) for mapping and samtools (http://www.htslib.org/) for duplicate removal (rmdup), sorting (sort) and indexing (index).
Coverage for each aligned ChIP-seq dataset (.bam) were computed with deeptools (https://deeptools.readthedocs.io/en/latest/index.html) and normalized using total read count for each sample. Coverage data were exported as bigwig (file format) for further processing.
Averaged ChIP-seq profiles were generated using the R package ggplot2. The x axis represents genomic position relative to DSB and the y axis represents the mean coverage at each bp. Heatmaps were generated by computeMatrix tool from deepTools.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: colorectum

extract_protocol:
For each precipitation, 1 × 10^7 cells were crosslinked by the addition of formaldehyde directly to the growth medium to a final concentration of 1%. After 10 min, crosslinking was quenched by the addition of glycine to a final concentration of 0.25 M at room temperature. Crosslinked cells were washed with PBS, scraped, and washed again with PBS containing 1 mM EDTA, and then lysed gently on ice for 5 min using 0.5 mL of ice-cold NP-40 lysis buffer. Cell lysates were added on top of a 1.25 mL sucrose cushion (24% sucrose (wt/vol) in NP-40 lysis buffer) and centrifuged at 12,000 rpm for 10 min at 4 °C to isolate the nuclei pellet. The chromatin pellet was washed twice with 1 mL PBS/1 mM EDTA, followed by centrifugation at 12,000 rpm for 1 min at 4 °C. The supernatant was discarded, the tube was pre-warmed at 37 °C for 2 min, and then 40 U MNase was added followed by incubation at 37 °C for 15 min with rotation at 700 rpm. Subsequently, the MNase was inactivated by the addition of 20 μL 0.5 M EDTA (to a final concentration of 10 mM) and 40 μL 0.5 M EGTA (to a final concentration of 20 mM). The mixture was then placed on ice, mixed thoroughly by pipetting, and sonicated using pre-cooled Biorupter at 15–20 x (30 s on/30 s off) on high position. The sonicated chromatin was spun down at 12,000 rpm for 10 min at 4 °C to collect the supernatant chromatin.
Sequencing libraries were prepared using 10 ng of purified DNA (average size 200–400 bp) using the NEBNext Ultra II Library Prep Kit for Illumina (E7645S, New England Biolabs)

treatment_protocol: we developed stable WT and ESCO2-depleted HCT116 cell lines expressing AsiSI, which is a restriction enzyme that targets an 8-bp recognition sequence, fused with estrogen receptor (ER) and HA tag (HA-ER-AsiSI cells). Since treatment with 4-hydroxytamoxifen (4-OHT) triggers the nuclear translocation of HA-ER-AsiSI and generates DSBs.

value: colorectum

value: colorectal cancer cell

value: 4-OHT treatment


title: TELC-D5.shLuc_rep1

status: Public on Dec 16 2023

type: SRA

city: guangzhou

first: Wenjuan

last: Li

state: 广东

address: UCAS

department: GIBH

country: China

institute: UCAS

library_source: transcriptomic

data_processing:
For bulk RNA-seq, reads were trimmed of adapters and low-quality reads were removed by fastp62 (v0.21.0) (https://github.com/OpenGene/fastp) with the default option.
Trimmed data were aligned to the Ensembl v76 (hg38) transcript annotations using STAR63 (v2.7.3a) with the settings “--outSAMtype BAM Unsorted, --quantMode TranscriptomeSAM, --outSAMheaderHD\@HD VN:1.4 SO:unsorted.”
Gene counts were calculated using RSEM (v1.2.18) with the settings “--paired-end.”
After removing the genes with zero count in all samples, DEG was determined using DESeq264 (v1.24) in R (v3.6.0).
Assembly: hg38
Supplementary files format and content: Text files include raw count, TPM values and FPKM values

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human naïve PSCs were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express and plated at a density of 100,000 cell/well of 6-well plate on Geltrex in TE induction medium (1:1 mix of Neurobasal medium (Gibco) and DMEM/F12 (HyClone) supplemented with N2 (Gibco) and B27 (Gibco), penicillin-streptomycin (HyClone), Glutamax (Gibco), β-mercaptoethanol (Sigma), 1 µM PD0325901 (Axon) and 1 µM A83-01 (Selleck)) for five days. TELCs at day 5 were used for downstream analysis throughout this study. For generating expandable TSCs, TELCs at day 5 were dissociated into single cells with TrypLE and plated on Geltrex-coated six-well plates at a 1:4-1:8 split ratio in TSC medium (DMEM/F12 supplemented with N2 and B27, penicillin-streptomycin, Glutamax, β-mercaptoethanol, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF (PeproTech), 0.5 µM A83-01 (Selleck), 1 µM SB431542 (Selleck), 2 µM CHIR99021 (Axon), 0.8 mM VPA (Vetec) and 5 µM Y-27632 (Axon)) supplemented with 10 µM Y-27632.

extract_protocol:
Total RNA was isolated using RNAzol (MRC) based on the manufacturer’s instructions.
Bulk RNA-seq library preparation and sequencing were performed at Berry Genomics (Beijing, China).

tag: cell line

tag: cell type

value: Human ESC derived-TELC-D5

tag: treatment

value: Luciferase knockdown (control)


title: OB neurons RBM20 KO_5

city: basel

first: peter

last: scheiffele

address: spitalstrasse 41

country: Switzerland

institute: Biozentrum, university of Basel

data_processing:
sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and RSeQC tool packages.
Reads were mapped using STAR (v2.4.0) (Dobin et al, 2013) on the mm10 Mouse genome assembly.
The input read count matrix was the same as used for the splicing analysis.
Two samples from the olfactory bulb were excluded from the analysis after the quality control of the data.
Read counts were summarized using featureCounts (Liao et al, 2014).
For each gene present in the FASTDB v2021_4 annotations, reads aligning on constitutive regions (that are not prone to alternative splicing) were counted.
Based on these read counts, normalization and differential gene expression were performed using DESeq2  (values were normalized to the total number of mapped reads of all samples) (Love et al, 2014) on R (v.3.5.3).
Genes were considered as expressed if their FPKM value is greater than 96% the background FPKM value based on intergenic regions.
The alternative splicing analysis was performed by calculating a splicing index (SI) which is the ratio of read density on the exon of interest and the read density on constitutive exons of the same gene.
Assembly: mm10
Supplementary files format and content: tables with the raw counts in FPKM, and the DGE and exon inclusion analysis for both PV and OB samples
Library strategy: Ribo-TRAP RNA-seq

molecule: polyA RNA

organism: Mus musculus

source_name: neurons

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: neurons

tag: genotype

value: KO


title: OB neurons RBM20 KO_1


title: OB neurons RBM20 KO_4


title: OB neurons RBM20 KO_2


title: OB neurons RBM20 KO_3


title: OB neurons RBM20 WT_5

value: WT


title: HCT116 AsiSI KD_SMC3

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: chip antibody

value: ac-SMC3(MABE1073, Millipore)


title: HCT116 AsiSI KD_53BP1


title: OB neurons RBM20 WT_3


title: OB neurons RBM20 WT_4


title: OB neurons RBM20 WT_2


title: HCT116 AsiSI WT_input


title: HCT116 AsiSI KD_rH2AX

value: rH2AX(ab81299, abcam)


title: TELC-D5.shVGLL1-4_rep2

value: VGLL1 knockdown


title: HCT116 AsiSI WT_53BP1


title: PV+ neurons RBM20 KO_4


title: PV+ neurons RBM20 KO_3


title: TSC.TEAD4_rep2

data_processing:
Library strategy: CUT&Tag
Raw sequence data were trimmed to remove both poor quality calls and adapters using fastp (v0.20.1) with the settings "--length_required=10 --n_base_limit=5".
Trimmed data were first aligned to the hg38 assembly using Bowtie2 (v2.2.5) with the settings “--very-sensitive.”
Low quality mapped reads were removed using Samtools with the settings “-q 30.” Duplicated reads were collapsed using Picard (v1.9.0).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files were generated from three replicates merged file using deeptools(v3.1.3) bamCoverage tool with --normalizeUsing CPM options.

source_name: TSC

growth_protocol: Cell culture: human naïve PSC were plated at a density of 100000 cells per well onextracellular matrix (ECM; Geltrex™)-coated 6-well plates and cultured with TE medium. TE medium was refreshed every two days. Cells were collected for RNA-seq on day 5. For human TSC cells, cells cultured in TS-1 medium for five or six days were plated on Collagen IV coated 6-well plates and cultured with TSC medium. Cells cultured in TSC medium became morphologically stable after 2-3 passages.

extract_protocol:
Cells（100,000）were incubated with Concanavalin A-coated magnetic beads, and then primary antibodies were added to incubate overnight at 4°C.
Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech , TD902-01) was used for CUT&Tag library construction.

value: H9 human naive pluripotent stem cell derived TSC


title: HCT116 AsiSI WT_rH2AX


title: Skin normal 33

type: genomic

city: Hanoi

first: Tham

middle: H

last: Hoang

address: Floor 9th, 458 Minh Khai

country: Viet Nam

institute: Vingroup Big Data Institute

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-33

hyb_protocol: RA1 resuspended DNA was loaded onto Infinium Asian Screening Array-24 v1.0 BeadChip . After incubation 16 - 24 hours at 48˚C, single-base extension and allele-specific staining was performed on a Te-flow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining the Beadchip was coated with XC4, dried for 1 hour and scanned by IScan Software (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using ASA-24 v1.0 Beadchip (Illumina).

label: Cy3, Cy5

source_name: Saliva

label_protocol: 250ng of genomic DNA was whole-genome amplified in an overnight reaction at 37˚C using amplification master mix (MA1, MA2 and MSM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from saliva was performed using MagMAX DNA Multi-Sample Ultra 2.0 Kit on KingFisher™ Flex Purification System.

tag: gender

value: F


title: TSC.TEAD4_rep1


title: PV+ neurons RBM20 KO_2


title: PV+ neurons RBM20 KO_1


title: TELC-D5.VGLL1_rep2

value: H9 human naive pluripotent stem cell derived TE


title: TELC-D5.TEAD4_rep1


title: TELC-D5.H3K27ac_rep2


title: TELC-D5.TEAD4_rep2


title: PV+ neurons RBM20 WT_1


title: HCT116 AsiSI WT_SMC3


title: TELC-D5.H3K27ac_rep1


title: TSC.ATAC_rep3

data_processing:
Raw sequence data were trimmed to remove both poor quality calls and adapters using fastp (v0.20.1) with the settings "--length_required=10 --n_base_limit=5".
Trimmed data were first aligned to the hg38 assembly using Bowtie2 (v2.2.5) with the settings “--very-sensitive.”
Low quality mapped reads were removed using Samtools with the settings “-q 30.” Duplicated reads were collapsed using Picard (v1.9.0).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files were generated from three replicates merged file using deeptools(v3.1.3) bamCoverage tool with --normalizeUsing CPM options.

extract_protocol:
Cells (50,000) were washed once with cold PBS and resuspended in 50 ml of lysis buffer [10 mM tris-HCl (pH 7.4) 10 mM NaCl, 3 mM MgCl2, and 0.1% (v/v) IGEPAL CA-630]. The suspension was then centrifuged at 500g for 10 min at 4°C, followed by addition of 50 ml of transposition reaction mix of the TruePrep DNA Library Prep Kit (Vazyme Biotech, TD502). Samples were then incubated at 37°C for 30 min.
Transposition reactions were cleaned up using the MinElute PCR Purification Kit (Qiagen, 28004). ATAC-seq libraries were subjected to five cycles for preamplification and amplified by PCR for an appropriate number of cycles. The amplified libraries were purified using the QIAquick PCR Purification Kit (Qiagen, 28104). Library concentration was measured using the VAHTSTM Library Quantification Kit (Vazyme Biotech, NQ101).


title: Heart, WT, size‐matched input, rep1

description: SMI

data_processing:
read1 were used for analysis.
For adapter trimming and low quality reads elimination, we used cutadapt 3.4 (-e 0.1 -O 1  --quality-cutoff 6 -m 18 -a AATAGCANNNNNAGATCGGAAGAGC -a ATATAGGNNNNNAGATCGGAAGAGC).
Trimmed and filtered reads were aligned to mm10 genome using STAR 2.7.9 (--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 -- outFilterScoreMin 10).
Aligned reads were deduplicated using dedup from UMI-tools 1.1.1
Peaks were called from aligned and deduplicated reads using clipper3.
Peaks were input-normalized and compressed using scripts from https://github.com/YeoLab/eclip
Peaks from replicates were merged using IDR software (https://github.com/nboley/idr), and further filtered with thresholds IDR < 0.05
Assembly: mm10
Supplementary files format and content: Appendix_table_S1.xlsx -table with the peak calling analysis for both OB and HR
Library strategy: seCLIP-Seq

source_name: Heart

growth_protocol: olfactory bulb or heart were obtained from 35 days old mice.

extract_protocol:
The CLIP experiments were performed according to the eCLIP protocol from Nostrand et al. (Van Nostrand et al., 2016) with some modifications. After IP, beads were washed 2x with the high salt wash buffer (50mM Tris-HCl pH7.5, 1M NaCl, 1mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate), 2x CLIP-lysis buffer, 2x with low salt wash buffer (20mM Tris-HCl pH7.5, 10mM MgCl2, 0.2% Tween-20) and 1x with PNK buffer 70mM Tris-HCl pH6.5, 10mM MgCl2). Beads were re-suspended in 100µl PNK-mix (70mM Tris-HCl pH6.5, 10mM MgCl2, 1mM DTT, 100U RNasin, 1U TurboDNase, 25U Polynucleotide-Kinase (NEB)) and incubated for 20min at 37°C in a thermomixer with shaking (1200 x rpm). After RNA dephosphorylation beads were washed as before with 2x high salt, 2x lysis and 2x low salt buffers and additionally with 1x Ligase buffer (50mM Tris-HCl pH7.5, 10mM MgCl2). Beads were re-suspended in 50µl ligase mix (50mM Tris-HCl pH7.5, 10mM MgCl2, 1mM ATP, 3 % DMSO, 15% PEG8000, 30U RNasin, 75U T4 RNA-ligase (NEB)). 10µl of the beads / ligase mix were transferred to a new tube and 1µl of pCp-Biotin (Jena Bioscience) were added to validate IP of the RNA-protein-complexes by western blot. To the rest (40µl) 4µl of the RNA-adaptor mix containing 40µM of each RNA_X1A & RNA_X1B (IDT) were added and samples were incubated for 2h at RT. After adaptor ligation samples were washed 2x with high salt, 2x with lysis and 1x with low salt buffers. Beads were re-suspended in 1x LDS sample buffer (Thermofisher) supplemented with 10 uM DTT and incubated at 65°C for 10min with shaking at 1200 x rpm. Eluates or inputs were loaded on 4-12% Bis-Tris, 10-well, 1.5mm gel (Thermofisher) and separated at 130V for ca. 1.5h. Proteins were transferred to the nitrocellulose membrane (Amersham) overnight at 30V. After transfer the membranes were placed in a 15cm Petri dish on ice and an area between 55 and 145kDa was cut out in small pieces and transferred to 2ml tube. For CLIP samples RNA extraction, reverse transcription using AR17 primer, cDNA clean-up using silane beads (Thermofisher), second adaptor ligation (rand103Tr3) and final cDNA purification were performed as previously described (Van Nostrand et al., 2016). For sized matched input samples (SMIn) isolated RNA was dephosphorylated. The sequencing libraries were amplified using Q5-DNA polymerase (NEB) and i50X/i70X Illumina indexing primers (IDT). The amplified libraries were purified and concentrated first with ProNEX size selective purification system (Promega) using sample/beads ratio of 1/2.4. The purified libraries were loaded on a 2% agarose gel, the area corresponding to the size between 175bp and 350bp was cut and the libraries were extracted from the gel using gel extraction kit (Machery&Nagel) and eluted with 16µl. Concentrations and size distributions of the libraries were determined on Fragment analyzer system (Agilent). 75bp paired-end sequencing was performed on the NextSeq500 platform using Mid Output Kit v2.5 (150 cycles).
Eric L. Van Nostrand et al. 2016, van Nostrand at al.; 2020

treatment_protocol: Tissue was dissected on ice, flash frozen in liquid nitrogen, and ground on dry ice. Frozen powder was UV-crosslinked 3x with 400mJ/cm2 on dry ice with a UV-crosslinker.

value: Heart


title: Heart, WT, size‐matched input, rep2

description: SMI


title: Spleen HSPC, Young, MPL-/-

city: Stony Brook

first: Huichun

last: Zhan

state: NY

address: 101 Nicolls Rd

country: USA

institute: Stony Brook Univeristy

data_processing:
Index of the reference genome was built using hisat2 2.1.0 and paired-end clean reads were aligned to the reference genome using HISAT2. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Differential gene expression analysis was performed using the DESeq R package (1.18.0). Genes with an adjusted p value < 0.05 found by DESeq were assigned as differentially expressed. Gene Ontology (GO) (http://www.geneontology.org/) and enrichment analysis of differentially expressed genes was implemented by the ClusterProfiler R package. GO terms with corrected p values < 0.05 were considered significantly enriched.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include gene ID, readcount, FPKM, log2 fold change, p value, padj value, and gene information for each sample

source_name: Spleen

extract_protocol:
Marrow and spleen Lin-cKit+ hematopoietic stem/progenitor cells (HSPCs) were isolated by magnetic bead isolation (with ~95% purity) (Miltenyi Biotec) from 3-4mo old wild-type (n=2), TPO-/- (n=3), and MPL-/- (n=3) mice. Total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 400ng of RNA was used to generate sequencing libraries using NEBNextÒ Ultra™ RNA Library Prep Kit for Illumina® (New England BioLabs, MA, USA) following manufacturer’s recommendations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform.

value: Spleen

value: Lineage-cKit+ HSPC

value: MPL-/-


title: Spleen HSPC, Young, TPO-/-

value: TPO-/-


title: OB neurons RBM20 WT_1


title: Marrow HSPC, Young, TPO-/-

source_name: Bone marrow

value: Bone marrow


title: Marrow HSPC, Young, MPL-/-


title: olfactory bulb, WT, size‐matched input, rep3

description: SMI

source_name: Olfacrory bulb

value: Olfacrory bulb


title: TSC.ATAC_rep2


title: TELC-D5.VGLL1_rep1


title: Heart, WT, eCLIP, rep1

description: eCLIP


title: olfactory bulb, WT, size‐matched input, rep2

description: SMI


title: Spleen HSPC, Young, Wild-type

value: Wild-type


title: PV+ neurons RBM20 WT_4

value: neurons


title: PV+ neurons RBM20 WT_3


title: olfactory bulb, WT, size‐matched input, rep1

description: SMI


title: olfactory bulb, WT, eCLIP, rep3

description: eCLIP


title: PV+ neurons RBM20 WT_2


title: TELC-D5.H3K27ac_rep3


title: TELC-D5.ATAC_rep3


title: Heart, WT, eCLIP, rep2

description: eCLIP


title: Marrow HSPC, Young, Wild-type


title: olfactory bulb, WT, eCLIP, rep2

description: eCLIP


title: TELC-D5.ATAC_rep2


title: siEzh2_2

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: mm10

source_name: aorta

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: aorta

value: VSMCs

value: Vascular smooth muscle cells


title: olfactory bulb, WT, eCLIP, rep1

description: eCLIP

value: WT


title: TELC-D5.ATAC_rep1


title: TSC.ATAC_rep1


title: siEzh2_1


title: Cre+ Day3, scRNAseq

city: Chongqing

first: taiping

last: Liu

address: Gaotanyan zhengjie 30, Shapingba district, Chongqing

institute: Department of Pathogenic Biology, Army Medical University (Third Military Medical University)

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: For scRNA-seq analysis, CD11b+ cells  were isolated from splenocytes of P. yoelii 17XNL-infected mice at day 0 and day 3 post-infection.

extract_protocol:
ATG5f/f LysM-Cre+ and ATG5f/f LysM-Cre- mice were inoculated intraperitoneally with 1 × 104 pRBCs. Then, CD11b+ cells were isolated from the spleens of ATG5f/f LysM-Cre+ and control mice using a mouse CD11b+ Cell Isolation Kit  at day 0 and day 3 post-infection.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
P. yoelii 17XNL infection
CD11b+ cells isolated from splenocytes

tag: strain

value: CD11b+ cells from splenocytes

tag: age

value: 6-8 weeks old

value: P. yoelii 17XNL-infected, day 3


title: Total RNA of Mtb mc2 cells after 10 min of streptomycin treatment batch2

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Mtb(NC_018143.2 ) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Assembly: Mycobacterium tuberculosis H37RV, NC_018143.2
Supplementary files format and content: wig files
Library strategy: SEnd-seq

organism: Mycobacterium tuberculosis

source_name: whole cell

growth_protocol: Mycobacterium tuberculosis (Mtb) H37Rv was grown at 37 °C in a minimal medium (Difco Middlebrook 7H9 broth) supplemented with 0.5% (v/v) glycerol, 0.05% (v/v) tyloxapol, 0.2 g L-1 casamino acids, 0.024 g L-1 pantothenic acid and 10% (v/v) OADC (BD). The double auxotrophic Mtb mc2 6206 strain (H37Rv ΔpanCD ΔleuCD)21 was grown in minimal medium with an additional 50 mg L-1 L-leucine (Sigma) and 24 mg mL-1 pantothenic acid (Sigma).

extract_protocol:
Bacterial cells were quenched by adding 1x vol of GTC buffer (600 g L-1 guanidium thiocyanate, 5 g L-1 N-laurylsarcosine and 7.1 g L-1 sodium citrate and 0.7% (v/v) 2-mercaptoethanol) to the culture medium immediately before the harvest and placed it at room temperature for 15 min. Cell pellets were collected by centrifugation (4,000 g for 10 min at 4 °C), then thoroughly resuspended in 100 μl of TE buffer (10 mM Tris-HCl and 1 mM EDTA, pH8.0). After adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and 300 mg of glass beads (Sigma, G1145), the cells were immediately lysed by bead beating with the Precellys Evolution homogenizer at the highest speed 10,000 rpm for 4x 45s cycles with interval of 60s at 4°C. Then the RNA was extracted following TRIzol RNA purification protocol.
SEnd-seq strategy was used to prepare the SEnd-seq library

treatment_protocol: RNA samples were collected when Mtb cells reached to log phase or stationary phase, or Mtb cells upon treatments of indicated antibiotics at different time points.

value: whole cell

value: bacterial cell

value: Streptomycin 10 min

tag: fraction

value: Nascent RNA


title: Control_2 (Ezh2 KD control)

value: Control


title: Control_3 (Ezh2 KD control)


title: Cre+ Day0, scRNAseq

description: 10x Genomics

value: Spleen

value: P. yoelii 17XNL-infected, day 0


title: spleen_apd1

city: Bethesda

first: Tim

last: Greten

state: Maryland

address: Building 10, Room 3B45, 9000 ROCKVILLE PIKE RM

department: TGMB

institute: NCI

description: 10x Genomics

data_processing:
Cell Ranger pipeline (version 6.1.2) was used to perform read depth normalization.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MC38-bearing mice

extract_protocol:
Liver and spleen lymphocyte are isolated from MC38-bearing mice. Staining was performed to identify the cell linage. FACS was performed a BD InsightInflux. Biological replicates were pooled as noted in the figure legend. CD3+CD4+GFP+ cells were lysed and partitioned.
Single-cell barcoding of reverse transcribed mRNA was performed on the Chromium controller. 3’ immune cell profiling chemistry v1.0 and v1.1 (10x Genomics, USA) was used. Single-cell cDNA amplification, and library preparation was proceeded via the manufacturer guidelines.

value: spleen

value: regulatory T cell

tag: Sex

value: female


title: spleen_isotype

description: 10x Genomics

value: isotype control


title: siEzh2_3

value: aorta

value: VSMCs


title: liver_isotype

description: 10x Genomics

value: liver


title: Cre- Day3, scRNAseq

description: 10x Genomics

value: CD11b+ cells from splenocytes


title: Control_1 (Ezh2 KD control)

value: Vascular smooth muscle cells


title: liver_apd1

description: 10x Genomics


title: Cre- Day0, scRNAseq

description: 10x Genomics

value: 6-8 weeks old


title: Genomic DNA from Metaplastic Breast Cancer 2

status: Public on Dec 15 2023

city: Sydney

first: Braydon

last: Meyer

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genetics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: Primary Metaplastic Breast Cancer

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 Beadchip using standard Illumina protocol

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

data_processing:
Data was processed in R using the 'minfi' package to read in and normalise data. PreprocessRaw was used to determine beta values
beta_detp.csv: average beta values
raw_detp.csv: unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Metaplastic Breast Cancer4245

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from all primary tumour samples using Qiagen QIAamp DNA FFPE Tissue Kit or MN Nucleospin DNA kit for FFPE, following the manufacturer’s instructions. The Infinium HD FFPE quality control and DNA restoration kits (Illumina, San Diego, CA, USA) were used to evaluate and repair degraded DNA samples where feasible

value: Female

tag: sample type

value: Metaplastic Breast Cancer

tag: grade

tag: sgh score

tag: age at diagnosis


title: Genomic DNA from Metaplastic Breast Cancer 1

description: Primary Metaplastic Breast Cancer

source_name: Metaplastic Breast Cancer3960


title: Genomic DNA from Phyllodes Tumour 29

description: Primary Phyllodes

source_name: Phyllodes Tumour 4413

value: Phyllodes

value: Malignant


title: Genomic DNA from Fibroadenoma 2

description: Primary Fibroadenoma

source_name: Fibroadenoma 4237

value: Fibroadenoma


title: CASE_2（KYSE510 cells_PAF_24 hours）

type: RNA

first: lingyuan

last: zhang

address: 52 Fucheng Road, Haidian District, Beijing, China

institute: BEIJING INSTITUTE FOR CANCER RESEARCH

description: whole gene exression

hyb_protocol: 1.5ug of Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/ug cRNA) was fragmented at 60 ℃ for 30 minutes in a reaction volume of 250 ml containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using Agilent Scanner G2505C.

data_processing: Data was extracted and normalized using Feature Extraction v10.7.1.1 software. Further Data analysis was performed using Agilent GeneSpring v13.1 software.

source_name: KYSE510 24H 100 nM PAF treatment.txt

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy  column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA was extracted using mirVanaTM RNA Isolation Kit (ABI, AM1561).

treatment_protocol: KYSE510 cells were treated with or without 100 nM PAF for 24 hours.

value: KYSE510 cells


title: Genomic DNA from Phyllodes Tumour 26

description: Primary Phyllodes

source_name: Phyllodes Tumour 4501


title: Genomic DNA from Phyllodes Tumour 27

description: Primary Phyllodes

source_name: Phyllodes Tumour 4503


title: Genomic DNA from Phyllodes Tumour 24

description: Primary Phyllodes

source_name: Phyllodes Tumour 4487


title: M-C 1h

city: Charlotte

first: Ehsan

last: Tabari

state: NORTH CAROLINA

address: 9201 University City Blvd

department: Bioinformatics

institute: UNC Charlotte

data_processing:
The genome sequence of E. coli K12 substr. MG1655 (NC_000913.2) was obtained from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/). The gene annotation file and the experimentally verified operons in the bacterium were downloaded from RegulonDB (Gama-Castro et al., 2011) (http://regulondb.ccg.unam.mx/). A total of 4,501 annotated genes (also including pseudo genes and non-coding small RNAs) are included in this analysis.
As the RNA-seq reads were not size-selected during the library construction to capture short RNAs, we trimmed the 3’ adapters attached to some short insertions. Adapter-free reads with lengths of <10 nucleotides (nt) were discarded, and the remaining reads were mapped to the E. coli K12 genome using Bowtie (Langmead et al., 2009). For the reads of length 10-14, 15-29 and ≥30 nt, up to 1, 2, and 3 mismatches were allowed, respectively. Only uniquely mapped reads were used for further analysis.
We used the assembly tool TruHmm to assemble transcripts in each sample with a window size = 11nt as described earlier (Li et al., 2013) except that we omitted the stitching step in TruHmm to reconstruct the ncRNAs or asRNAs.
In addition, we used DAVID (Dennis et al., 2003) to analyze functional annotation enrichment for groups of genes.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: tab-separated files that each line represent an operon or a gene, columns are titled in the files. logNT and senseLogNT are RKPM values. List items are separated by double dots (..).

organism: Escherichia coli K-12

source_name: M-C 1h

growth_protocol: A frozen stock of Escherichia coli K12 strain MG1655 was thawed, inoculated in LB medium in a test tube by 1:100 dilution and cultured overnight at 37 oC and 250 rpm. The cells were then transferred to fresh LB medium in a flask by 1:100 dilutions, and cultured at 37 oC and 250 rpm. When the cells grew to an optical density at 610 nm (OD610) of 1.0, they were spun down at 3,200g for 25 min.

extract_protocol:
RNA was isolated from the samples using RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10g total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA, and the complete removal of DNA was confirmed  by 35 cycles PCR amplification of a 196 bp fragment of the crp gene (5’-primer:AGCATATTTCGGCAATCCAG;3’-primer:TACAGCGTTTCCGCTTTTTC).  rRNAs were depleted from the total RNA using a MICROBExpress kit (Ambion) to enrich mRNAs.
In our earlier experiments, sequencing was done on an Illumina GAII platform at the sequencing core facility of the University of North Carolina at Chapel Hill, and the directional RNA-seq libraries were constructed using Illumina Small RNA Sample Prep Kit following the vendor’s instruction with some modifications. Briefly, after the purified mRNA was fragmented using a RNA fragmentation kit (Ambion), the fragmented RNA was treated with Antarctic phosphatase (NEB) to remove the 5’-tri-phosphate groups of RNAs with an intact 5’-end. A mono-phosphate group was then added back to the 5’-end of RNAs by polynucleotide kinase (PNK, NEB) in the presence of 10 mM ATP.  The v1.5 sRNA 3’ Adaptor  (5'/5rApp/ ATCTCGTATGCCGTCTTCTGCTTG /3ddC/) was ligated to the 3’-end of fragmented RNAs using truncated T4 ligase 2 (NEB), and the SRA 5’ RNA adaptor (5'GUUCAGAGUUCUACAGUCCGACGAUC) was ligated to the 5’-end of fragmented RNAs using T4 ligase. To preserve short inserts from small RNAs we omitted the size selection step after PCR application of the inserted RNA fragments. For our later experiments, sequencing was done on an Illumina HiSeq 2000 platform at David H. Murdock Research Institute of the North Carolina Research Campus (Kannapolis, NC), and we constructed the directional RNA-seq libraries using Illumina’s TruSeq Small RNA Sample Prep Kit, so that multiplex sequencing can be achieved by using the barcoded PCR primers. The details of the method will be described elsewhere (Dong, Li and Su).  Briefly, after similar treatments as described above, the 5’ Adapter (RA5: 5’ GUUCAGAGUUCUACAGUCCGACGAUC), and 3’ Adapter (RA3: 5’ TGGAATTCTCGGGTGCCAAGG) were ligated to 5’- and 3’-end of fragmented RNAs, respectively. Reverse transcription-PCR (RT-PCR) was performed using SuperScript II Reverse Transcriptase Kit (Invitrogen) using the SRA RT primer, followed by 16 cycles of PCR amplification. Again, the size selection was omitted on PCR products to preserve short inserts from possible small RNAs. Single-end sequencing on the Illumina GA II platform was done with 76 cycles, while that on the HiSeq 2000 platform was done with 100 cycles. Libraries for some samples (M-C1h and M-C2h) were prepared by the two methods and sequenced on the two different platforms.

treatment_protocol: For the minimal medium MOPS culture (MOPS), the cell pellets were resuspended in the same volume of MOPS medium (100 ml of 10X MOPS mixture, 880ml of sterile H2O, 10ml (0.132M) KH2PO4 and 10ml of 20% glucose, Teknova, Hollister, CA). For heat shock treatment (HS), the cell pellets were resuspended in the same volume of MOPS medium, and incubated at 48oC and 250 rpm. For phosphorus-starvation treatment (M-P), the cell pellets were resuspended in the MOPS medium without KH2PO4. For carbon-starvation treatment (M-C), the cell pellets were resuspended in the MOPS medium without glucose. Each culture was done in three replicates in parallel, and an equal volume of cells was collected from each replicate to minimize experimental variations during sampling. Three and 20 ml of the mixed cell suspension were collected for transcriptome and proteome analyses, respectively, at each desired time points (HS:15min, 30min, 1h, 2hrs and 4hrs; MOPS, M-C and M-P: 1hr, 2hrs, 4hrs  6hrs; M-C: 1hr, 2hrs, 4hrs, 6hrs). For the LB culture, samples were collected when the cell suspension OD610 reached to 0.5, 1.0 and 3.  For transcriptome analysis, the collected cells were immediately mixed with 1.5ml RNA Later (Invitrogen) and spun down at 6,000g for 8 min (-4 oC). The pellets were resuspended in 1.5 ml of RNAlater, and stored at -80 oC until use.

tag: condition

value: carbon-starvation treatment


title: Genomic DNA from Phyllodes Tumour 28

description: Primary Phyllodes

source_name: Phyllodes Tumour 4506


title: Genomic DNA from Phyllodes Tumour 25

description: Primary Phyllodes

source_name: Phyllodes Tumour 4488


title: Total RNA of Mtb mc2 cells after 10 min of DMSO treatment batch2

value: whole cell

value: bacterial cell

value: WT

value: DMSO 10 min

value: Nascent RNA


title: Genomic DNA from Phyllodes Tumour 23

description: Primary Phyllodes

source_name: Phyllodes Tumour 4486


title: Genomic DNA from Phyllodes Tumour 22

description: Primary Phyllodes

source_name: Phyllodes Tumour 4480


title: control（KYSE510 cells_24 hours_control）

description: whole gene exression

source_name: KYSE510 24H control.txt


title: Total RNA of Mtb mc2 cells after 10 min of clarithromycin treatment batch2

value: Clarithromycin 10 min


title: Genomic DNA from Phyllodes Tumour 19

description: Primary Phyllodes

source_name: Phyllodes Tumour 4003


title: Genomic DNA from Phyllodes Tumour 18

description: Primary Phyllodes

source_name: Phyllodes Tumour 4235


title: Genomic DNA from Phyllodes Tumour 20

description: Primary Phyllodes

source_name: Phyllodes Tumour 4321


title: Genomic DNA from Phyllodes Tumour 21

description: Primary Phyllodes

source_name: Phyllodes Tumour 4436


title: Genomic DNA from Phyllodes Tumour 15

description: Primary Phyllodes

source_name: Phyllodes Tumour 4004


title: Genomic DNA from Phyllodes Tumour 16

description: Primary Phyllodes

source_name: Phyllodes Tumour 4025


title: Genomic DNA from Phyllodes Tumour 12

description: Primary Phyllodes

source_name: Phyllodes Tumour 3490


title: Genomic DNA from Phyllodes Tumour 17

description: Primary Phyllodes

source_name: Phyllodes Tumour 4030


title: M-C 2h

source_name: M-C 2h


title: Genomic DNA from Phyllodes Tumour 13

description: Primary Phyllodes

source_name: Phyllodes Tumour 3976


title: Genomic DNA from Fibroadenoma 1

description: Primary Fibroadenoma

source_name: Fibroadenoma 4236


title: Genomic DNA from Phyllodes Tumour 11

description: Primary Phyllodes

source_name: Phyllodes Tumour 4504

value: Borderline


title: Genomic DNA from Phyllodes Tumour 9

description: Primary Phyllodes

source_name: Phyllodes Tumour 4489


title: Genomic DNA from Phyllodes Tumour 5

description: Primary Phyllodes

source_name: Phyllodes Tumour 3980


title: Genomic DNA from Phyllodes Tumour 10

description: Primary Phyllodes

source_name: Phyllodes Tumour 4502


title: Genomic DNA from Phyllodes Tumour 7

description: Primary Phyllodes

source_name: Phyllodes Tumour 4012


title: Genomic DNA from Phyllodes Tumour 2

description: Primary Phyllodes

source_name: Phyllodes Tumour 3996

value: Benign


title: Genomic DNA from Phyllodes Tumour 4

description: Primary Phyllodes

source_name: Phyllodes Tumour 3975


title: Genomic DNA from Phyllodes Tumour 1

description: Primary Phyllodes

source_name: Phyllodes Tumour 4018


title: Genomic DNA from Phyllodes Tumour 6

description: Primary Phyllodes

source_name: Phyllodes Tumour 4005


title: Genomic DNA from Phyllodes Tumour 3

description: Primary Phyllodes

source_name: Phyllodes Tumour 3972


title: Genomic DNA from Phyllodes Tumour 8

description: Primary Phyllodes

source_name: Phyllodes Tumour 4028


title: Excluded due to poor quality. Microglia from adult CNS Sample 11

city: Solna

first: Rasmus

middle: Par Arild Oskar

last: Berglund

state: Sweden

address: CMM L8:04, Neuroimmunology

department: Clinical neuroscience

country: Sweden

institute: Karolinska institute

description: CD11B, P-ERK1/2  Thr202/Thyr204 , CD45, Ly6G

hyb_protocol: Cells were stained with surface antibodies (CD11b, Ly6G, CD45) and intracellular ERK1/2- at Thr202/Thyr204 after permabilization and fixation

scan_protocol: Cells were MACS sorted with CD11b and for separating P-ERK1/2 Thr202/Thyr204 high and low further sorted with  a BD Influx cell sorter based on

data_processing: Cells were prepared and analyzed in Nanostring nCounter system using the Neuroinflammation panel detecting 770 genes. GPL33016

label: NanoString

source_name: Microglial cells, fixed in PFA

label_protocol: Cells were sorted based on CD11b marker and aged CNS sorted further discriminated by phorphorylation of ERK1/2- at Thr202/Thyr204

growth_protocol: Aged mice refer to > 80 weeks old, adult refer to 12-20 weeks old

extract_protocol: Mice were eutanized with CO2, CNS dissected and single cell suspension were pepared using the Miltenyi Neural tissue dissection (T) kit according to instructions. Cells were then fixed and permeabilized for labeling with antibodies prior to sorting.

treatment_protocol: Mice and cells were untreated

value: Brain, microglia, aged, ERK

value: C57B6 mice


title: Genomic DNA from Phyllodes Tumour 14

description: Primary Phyllodes

source_name: Phyllodes Tumour 3983

value: Female


title: P-ERK1/2 Low microglia from aged mouse CNS Sample 9


title: P-ERK1/2 high microglia from aged mouse CNS Sample 8


title: W12E_Prol_145_PRO-seq_2

city: Dallas

first: Cheng-Ming

last: Chiang

state: Texas

address: 6001 Forest Park Road

department: Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

description: Proliferation, pBRD4i 145, nascent RNA profiling

data_processing:
150 bp paired-end reads in fastq files were checked for quality using FastQC (v0.11.2). Reads were trimmed using TrimGalore v0.6.0 .
Trimmed reads were aligned using bowtie v1.2.393 to a concatenated genome containing the HPV16 (K02718.1), D. melanogaster (UCSC assembly dm6), and human (UCSC assembly hg38) genomes. Duplicates were marked using SAMBAMBA and removed.
BAM files were converted into bedGraphs with bedtools genomecov v2.27.1. Read counts were corrected by taking into considering the library size and total spike-in reads before generating bigWig tracks.
A raw count matrix was generated for reads overlapping with the longest transcript. Genes with at least 25 counts in any of the replicates for each pairwise comparison (DMSO vs treatment) were kept. Normalized read counts and differentially expressed genes were generated using EdgeR v3.34.
Assembly: hg38
Supplementary files format and content: PRO-seq strand-specific bigwig tracks

growth_protocol: Proliferating W12E cells were cultured without feeder cells at sub-confluence in low-calcium (0.05 mM) F-medium. Differentiated W12E cells were cultured in EGF-free high-calceium (1.4 mM) F-medium upon confluence.

extract_protocol:
Nuclei from W12E cells and Drosophila Schneider 2 (S2) were isolated using the permeabilization buffer.
cDNA libraries were constructed by 3’ RNA adaptor ligation, 5’ phosphorylation, decapping, and 5’ RNA adaptor ligation with subsequent reverse transcription and PCR amplification.

treatment_protocol: Cells were treated by 5 µM of pNPS14, 1 µM of pNPS90, pNPS145, or JQ1, or DMSO-only for 4 hours before harvest.

value: HPV16-positive cervical keratinocyte

value: wildtype

value: Proliferation, pNPS145


title: P-ERK1/2 high microglia from aged mouse CNS Sample 7


title: P-ERK1/2 Low microglia from aged mouse CNS Sample 12


title: Microglia from adult CNS Sample 4


title: P-ERK1/2 Low microglia from aged mouse CNS Sample 3


title: W12E_Prol_145_PRO-seq_1


title: Microglia from adult CNS Sample 10


title: W12E_Prol_JQ1_PRO-seq_2

description: Proliferation, BBDi JQ1, nascent RNA profiling

value: Proliferation, JQ1


title: P-ERK1/2 Low microglia from aged mouse CNS Sample 6


title: W12E_Prol_JQ1_PRO-seq_1


title: P-ERK1/2 high microglia from aged mouse CNS Sample 5


title: W12E_Prol_90_PRO-seq_1

description: Proliferation, pBRD4i 90,nascent RNA profiling

value: Proliferation, pNPS90


title: P-ERK1/2 high microglia from aged mouse CNS Sample 2

source_name: Fixed P-ERK1/2 high microglia from aged mouse CNS


title: W12E_Prol_14_PRO-seq_1

description: Proliferation, pBRD4i 14, nascent RNA profiling

value: Proliferation, pNPS14


title: Microglia from adult CNS Sample 1

source_name: Fixed microglia from adult CNS


title: W12E_Diff_145_PRO-seq_2

description: Differentiation, pBRD4i 145, nascent RNA profiling

value: Differentiation, pNPS145


title: W12E_Diff_JQ1_PRO-seq_2

description: Differentiation, BBDi JQ1, nascent RNA profiling

value: Differentiation, JQ1


title: W12E_Diff_14_PRO-seq_2

description: Differentiation, pBRD4i 14, nascent RNA profiling

value: Differentiation, pNPS14


title: W12E_Diff_JQ1_PRO-seq_1


title: W12E_Prol_DMSO_PRO-seq_2

description: Proliferation, DMSO, nascent RNA profiling

value: Proliferation, DMSO


title: W12E_Prol_DMSO_PRO-seq_1


title: W12E_Diff_145_PRO-seq_1


title: W12E_Diff_90_PRO-seq_2

description: Differentiation, pBRD4i 90,nascent RNA profiling

value: Differentiation, pNPS90


title: W12E_Prol_90_PRO-seq_2


title: W12E_Diff_DMSO_PRO-seq_2

description: Differentiation, DMSO, nascent RNA profiling

value: Differentiation, DMSO


title: W12E_Diff_14_PRO-seq_1


title: differentiated HL-60, 1 µg/ml LTA, 24 hour, rep-1

city: Kaohsiung

first: Meng-Chi

last: Yen

address: No.100, Shih-Chuan 1st Road

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program fastp (version 0.20.0).
The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0).
The software FeatureCounts (v2.0.1) in Subread package was applied for the quantification of the gene abundance.
Differentially expressed genes (DEGs) were identified by DESeq2 (version 1.28.0) or EdgeR (version 3.36.0)
Assembly: Homo_sapiens.GRCh38.98
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted with a Total RNA Purification Kit (Norgen Biotek).  1 μg total RNA was used for construction of sequencing libraries.
The sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations.

value: human promyelocytic leukemia cell

value: WT, differentiated

value: 1 μg/ml Staphylococcus aureus lipoteichoic acids

tag: time

value: 24 hours


title: undifferentiated HL-60, untreated control, 24 hour

tag: cell line

value: WT, undifferentiated

value: untreated


title: undifferentiated HL-60, 1 µg/ml LTA, 24 hour

tag: cell type


title: undifferentiated HL-60, untreated control, 4 hour

tag: treatment

value: 4 hours


title: undifferentiated HL-60, 1 µg/ml LTA, 4 hour

tag: genotype


title: differentiated HL-60, 10 µg/ml LTA, 4 hour, rep-1

value: 10 μg/ml Staphylococcus aureus lipoteichoic acids


title: differentiated HL-60, untreated control, 24 hour, rep-2


title: differentiated HL-60, 1 µg/ml LTA, 4 hour, rep-2


title: differentiated HL-60, 10 µg/ml LTA, 24 hour, rep-2


title: differentiated HL-60, 1 µg/ml LTA, 24 hour, rep-2


title: differentiated HL-60, 10 µg/ml LTA, 4 hour, rep-2


title: W12E_Prol_14_PRO-seq_2

value: HPV16-positive cervical keratinocyte

value: wildtype


title: differentiated HL-60, untreated control, 24 hour, rep-1


title: W12E_Diff_90_PRO-seq_1


title: differentiated HL-60, 1 µg/ml LTA, 4 hour, rep-1


title: differentiated HL-60, untreated control, 4 hour, rep-2


title: s1366_STIM_human_PHA

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description:
s1366_STIM
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt

data_processing:
Partek Flow software, version 10.0
Raw data were filtered by removing reads containing adapters and reads containing N > 10% and for Phred scores >30
Filtered reads were aligned with STAR 2.7.3a, using either CanFam3.1 genome assembly or GRCh38 human genome assembly
Aligned reads were annotated and counted using HT-seq  with Ensembl 104 for CanFam3.1 and release 107 for GRCh38
differentially expressed genes were identified using DEseq2
Assembly: CanFam3.1 genome assembly or GRCh38 human genome assembly
Supplementary files format and content: tab-delimited text files include CPM normalized counts

source_name: Blood

growth_protocol: Following Ficoll separation, PBMC for both species were washed with PBS, counted and added to 24-well plates in triplicate cultures, at a cell density of 2 X 10^6 cells per mL in complete culture medium.  Cell culture medium consisted of DMEM supplemented with amino acids (essential and non-essential), 1% penicillin-streptomycin, Glutamax (ThermoFisher Scientific, Waltham, MA) and 10% fetal bovine serum (Peak Serum, Inc, Wellington, CO).  For T cell activation, phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml for 24h (RNA sequencing).

extract_protocol:
RNA was extracted from cells using Qiagen RNeasy mini kit
the mRNA was purified using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was completed following end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: tissue

value: Blood

value: primary tissue

value: PBMC

value: PHA


title: W12E_Diff_DMSO_PRO-seq_1


title: s1918_STIM_human_PHA

description:
s1918_STIM
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt

treatment_protocol: phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml


title: s1240_human_ctrl

description:
s1240
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: s1366_human_ctrl

description:
s1366
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: differentiated HL-60, untreated control, 4 hour, rep-1


title: s1781_STIM_human_PHA

description:
s1781_STIM
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: s1515_STIM_human_PHA

description:
s1515_STIM
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: s1240_STIM_human_PHA

description:
s1240_STIM
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: s1515_human_ctrl

description:
s1515
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: differentiated HL-60, 10 µg/ml LTA, 24 hour, rep-1


title: s1918_human_ctrl

description:
s1918
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt


title: Normal-5

city: beijing

first: Junjie

last: Luo

address: 2 West Yuanmingyuan Road, Haidian District

institute: China Agricultural University

data_processing:
For 10x data, Cell Ranger 5.0.0 was used to quantify gene expression level and to identify TCR sequences with human reference version GRCh38.
The output of Cell Ranger filtered gene expression matrics were analyzed by R software (Version 3.6.1) with the Seurat package (Version 3.2.0).
Before the downstream analysis, low-quality cells were excluded and retained the high-quality single-cell data that met the following criterial: 1) cell with the number of detected genes was greater than 800 and less than 6000; 2) cell with the percentage of gene derived from the mitochondrial genome less than 10%.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Vascular cells

extract_protocol:
Aortic tissues were cut into approximately 1-2 mm3 pieces in an enzyme cocktail and were digested at 37℃ for 60 min. The dissociated cells were subsequently passed through a 70 µm SmartStrainer and centrifuged at 400 g for 5 min. After washing twice with 1× PBS, the cell pellets were re-suspended in sorting buffer.
Cells were loaded 16500 cells/chip position using the 10x Chromium Next GEM Single Cell 5' Kit v2. All the subsequent steps were performed following the standard manufacturer’s protocols.

value: ascending aorta

value: Female

tag: group

value: normal


title: Normal-1

tag: gender


title: Aortic dissection Subacute-3

value: Male

value: Subacute


title: Normal-2


title: Aortic dissection Subacute-1


title: Aortic dissection Acute-3

value: Acute


title: Aortic dissection Chronic-2

value: Chronic


title: Aortic dissection Acute-2


title: Aortic dissection Acute-4


title: in vitro attached human blastoids d10

city: New York

first: Riccardo

last: De Santis

address: 1230 York Ave

institute: The Rockefeller univeristy

description: scRNA-seq data

data_processing:
FASTQ file were aligned using Cell Ranger (7.0.0) against hg38 reference genome.
Count matrix were further processed using Python in the Scanpy environment (https://pypi.org/project/scanpy/)
The raw matrices were filtered to have a minimum of 300 detected genes per cell and genes were filtered to be expressed in at least 3 cells.
Cells with over 20% mitochondrial UMIs were discarded.
Clustering analysis was performed using Leiden algorithm on normalized counts and visualized in a low-dimensional space using UMAP plots
Assembly: Hg38
Supplementary files format and content: We uploaded the Cell ranger count matrix and cluster annotation in the metadata csv.

source_name: ES-derived cells

growth_protocol: Naïve human pluripotent stem cell are differentiated in Aggrewells with PALLY-LY media for 4 days, individual blastoids were manually picked and transferred on Laminin 521 coated dishes in IVC1 media (48h) and then IVC2 media supplemented with ROCK-inhibitor

extract_protocol: 10X genomics v3 3 prime library

treatment_protocol: Application of extracellular matrix (geltrex 5%) is started at 5 days post attachement

value: ES-derived cells

value: ectoderm, mesoderm and endoderm and extra-embryonic cells

value: XX

value: differentiation in IVC1-IVC2 media

value: day 10


title: Aortic dissection Chronic-1


title: in vitro attached human blastoids d7

description: scRNA-seq data

value: day 7


title: Aortic dissection Subacute-2


title: NF2KO, IFNg, RepC

city: St. Louis

first: Sumit

middle: Kumar

last: Matta

state: MO

address: 660 S. Euclid

department: Molecular Microbiology

institute: Washington University in St. Louis

description: r.CATTCTAGGT-TACGAATCGA.HHYJHDSX2_CATTCTAGGT-TACGAATCGA_L003_R1_GE

data_processing:
Reads were sequenced on Illumina NovaSeq-6000 sequencer. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software
RNA-Seq-Analysis built-in tool of  CLCGenomics Workbench ver 21.0.5 (QIAGEN Bioinformatics, Inc.) was used to map the reads to Homo sapiens hg38 reference genome resulting in gene expression (GE) and transcript expression (TE) tracks for each sample.
Differential expression for RNA-Seq built-in tool of CLCGenomics Workbench ver 21.0.5 was used to calculate fold difference in total counts between different samples (using gene expression tracks or (GE).clc files).
Assembly: hg38
Supplementary files format and content: Gene expression and transcript expression tracks ((GE).clc and (TE).clc) were generated using RNA-Seq-Analysis tool in CLCGenomics Workbench ver 21.0.5.  Expression_Values.csv is the expression table for all 60,676 annotated human genes across all samples and replicates.

source_name: NF2KO, IFNg

growth_protocol: A549 cells were maintained in Dulbecco's modified eagle medium (DMEM) with 10% v/v fetal bovine serum (FBS) at 37 ⁰C and 5% CO₂.

extract_protocol:
Samples were lysed, and RNA was extracted using QIAGEN RNeasy mini kit per manufacturer’s instructions. Total RNA was then submitted to Genome Technology Access Center (GTAC), Washington University in St. Louis, School of Medicine for Next generation mRNA sequencing.
Briefly, library preparation was performed using ~ 1ug of total RNA processed using RiboErase kits to remove ribosomal RNA (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degree Celsius for 8 min. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) using random hexamers. A second strand reaction was performed to yield ds-cDNA that was blunt ended, extended by adding an A base to the 3' ends, and followed by ligation of Illumina sequencing adapters. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 to generate paired end reads extending 150 bases.

treatment_protocol: A549 cells were seeded in a 6-well plate overnight. The cells were then left untreated or treated with IFN-gamma (100 U/ml) for 24 h.

value: Epithelial (Lung)

value: IFN-γ

tag: replicate

value: C


title: Aortic dissection Acute-1


title: s1781_human_ctrl

description:
s1781
Partek_human_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt

value: Blood

value: primary tissue

value: PBMC

value: untreated


title: NF2KO, Control, RepC

description: q.AGCGAAGCTG-CTCTGATTCA.HHYJHDSX2_AGCGAAGCTG-CTCTGATTCA_L003_R1_GE

source_name: NF2KO, Control

value: Control


title: WT, IFNg, RepC

description: n.GTAACGTCAC-ACCAACTAAG.HHYJHDSX2_GTAACGTCAC-ACCAACTAAG_L003_R1_GE

source_name: WT, IFNg

value: WT


title: IRF1KO, IFNg, RepC

description: p.AGGCCATTGA-GCATGTGCGT.HHYJHDSX2_AGGCCATTGA-GCATGTGCGT_L003_R1_GE

source_name: IRF1KO, IFNg


title: Normal-4

value: ascending aorta

value: Male

value: normal


title: WT, Control, RepC

description: m.AACATCTCGA-TATTCGCCAG.HHYJHDSX2_AACATCTCGA-TATTCGCCAG_L003_R1_GE

source_name: WT, Control


title: NF2KO, IFNg, RepB

description: l.AATGACAAGG-TTCGAGGTTG.HHYJHDSX2_AATGACAAGG-TTCGAGGTTG_L003_R1_GE

value: B


title: Normal-3


title: IRF1KO, IFNg, RepB

description: j.GTCAACGTAA-ACAGGTAGAA.HHYJHDSX2_GTCAACGTAA-ACAGGTAGAA_L003_R1_GE


title: IRF1KO, Control, RepB

description: i.ACTTACCAAC-GATCAAGCCA.HHYJHDSX2_ACTTACCAAC-GATCAAGCCA_L003_R1_GE

source_name: IRF1KO, Control


title: NF2KO, Control, RepB

description: k.AGAAGATTGG-CTTCCTACAA.HHYJHDSX2_AGAAGATTGG-CTTCCTACAA_L003_R1_GE


title: IRF1KO, IFNg, RepA

description: d.TGAACGTTAC-CTTGCTATTC.HHYJHDSX2_TGAACGTTAC-CTTGCTATTC_L003_R1_GE

value: A


title: WT, Control, RepA

description: a.AGGCTCATCG-ATCATACCGC.HHYJHDSX2_AGGCTCATCG-ATCATACCGC_L003_R1_GE


title: NF2KO, Control, RepA

description: e.AGGACGTCTC-GAGGATGCGA.HHYJHDSX2_AGGACGTCTC-GAGGATGCGA_L003_R1_GE


title: HctYC_OM3B_8-6-J7-P24

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

source_name: OM3B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: HctYC_OM3B_8-6-J7-P23

tag: Sex


title: HctYC_OM3B_8-6-J7-P12


title: HctYC_OM3B_8-6-J7-P11


title: WT, IFNg, RepB

description: h.CGCAACATGC-ATACGAAGCA.HHYJHDSX2_CGCAACATGC-ATACGAAGCA_L003_R1_GE


title: WT, Control, RepB

description: g.AGAAGACCTA-GATAGGTTGC.HHYJHDSX2_AGAAGACCTA-GATAGGTTGC_L003_R1_GE


title: HctYC_OM3B_8-6-J7-O24


title: NF2KO, IFNg, RepA

description: f.CACGTTACTC-TACCTTATGC.HHYJHDSX2_CACGTTACTC-TACCTTATGC_L003_R1_GE


title: WT, IFNg, RepA

description: b.TCAACGCGTA-ATGACAGCAC.HHYJHDSX2_TCAACGCGTA-ATGACAGCAC_L003_R1_GE


title: IRF1KO, Control, RepA

description: c.TCTCACCAGG-ATGGCGCCTT.HHYJHDSX2_TCTCACCAGG-ATGGCGCCTT_L003_R1_GE


title: HCT116 _TRPS1(WT)

first: wenjie

last: liu

address: No. 17 Nanli, Panjiayuan, Chaoyang District

institute: National Cancer Center/National Clinical  Research Center for Cancer/Cancer  Hospital

data_processing:
Diluted pAG-Tn5 adapter complex was then added followed by the tagmentation reaction. Extracted DNA fragments were used for library preparation.
The libraries were sequenced by Novogene using the Illumina NovaSeq 6000 platform
DNA sequencing raw reads were preprocessed by filtering outsequencing adapters, short-fragment reads and other low-quality reads
Bowtie (version 0.12.8) was then used to map the clean reads to the human hg19 reference genome.
Peak detection was performed by MACS with a minimum P-value cut-off of 0.00001 (version 1.4.2, https://pypi.python.org/pypi/MACS/1.4.2).
The peak recognition, overlap, subtraction, merge and feature annotation analysis of enriched regions were performed by using the Hypergeometric Optimization of Motif EnRichment 2 (HOMER2) suite (version 3.0, http://homer.ucsd.edu/homer/).
Motif-density histograms were created using HOMER for target regions and promoters defined as −2 kb to +1 b relative to the TSS
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT & Tag-Seq

growth_protocol: IMDM, 10% fetal bovine serum,1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
cells were incubated with activated NovoNGSR ConA Beads. The bead-bound cells were permeabilized and incubated first with Flag   primary antibody , followed by anti-rabbit antibody.
The CUT & Tag assay was performed using the NovoNGS® CUT & Tag 3.0 High-Sensitivity Kit  according to manufacturer’s protocols

value: epithelial

tag: chip antibody


title: HCT116 _TRPS1(R544Q)


title: IRF1KO, Control, RepC

description: o.GCTAACCGTG-TCACCATAAG.HHYJHDSX2_GCTAACCGTG-TCACCATAAG_L003_R1_GE

value: Epithelial (Lung)


title: HctYC_OM3B_8-6-J7-O23


title: HctYC_OM3B_8-6-J7-N24


title: HctYC_OM3B_8-6-J7-N11


title: HctYC_OM3B_8-6-J7-L24


title: HctYC_OM3B_8-6-J7-M11


title: HctYC_OM3B_8-6-J7-O12


title: HctYC_OM3B_8-6-J7-O11


title: HctYC_OM3B_8-6-J7-L12


title: HctYC_OM3B_8-6-J7-N23


title: HctYC_OM3B_8-6-J7-N12


title: HctYC_OM3B_8-6-J7-M23


title: HctYC_OM3B_8-6-J7-L11


title: HctYC_OM3B_8-6-J7-L23


title: HctYC_OM3B_8-6-J7-M12


title: HctYC_OM3B_8-6-J7-J24


title: HctYC_OM3B_8-6-J7-M24


title: HctYC_OM3B_8-6-J7-K24


title: HctYC_OM3B_8-6-J7-K11


title: HctYC_OM3B_8-6-J7-I24


title: HctYC_OM3B_8-6-J7-I11


title: HctYC_OM3B_8-6-J7-K12


title: HctYC_OM3B_8-6-J7-J23


title: HctYC_OM3B_8-6-J7-H23


title: HctYC_OM3B_8-6-J7-H11


title: HctYC_OM3B_8-6-J7-G24


title: HctYC_OM3B_8-6-J7-I23


title: HctYC_OM3B_8-6-J7-J12


title: HctYC_OM3B_8-6-J7-I12


title: HctYC_OM3B_8-6-J7-H12


title: HctYC_OM3B_8-6-J7-H24


title: HctYC_OM3B_8-6-J7-K23


title: HctYC_OM3B_8-6-J7-J11


title: HctYC_OM3B_8-6-J7-G23


title: HctYC_OM3B_8-6-J7-F11


title: HctYC_OM3B_8-6-J7-E24


title: HctYC_OM3B_8-6-J7-E23


title: HctYC_OM3B_8-6-J7-G11


title: HctYC_OM3B_8-6-J7-F24


title: HctYC_OM3B_8-6-J7-F12


title: HctYC_OM3B_8-6-J7-F23


title: HctYC_OM3B_8-6-J7-D11


title: HctYC_OM3B_8-6-J7-D24


title: HctYC_OM3B_8-6-J7-D12


title: HctYC_OM3B_8-6-J7-E12


title: HctYC_OM3B_8-6-J7-E11


title: HctYC_OM3B_8-6-J7-C23


title: HctYC_OM3B_8-6-J7-B12


title: HctYC_OM3B_8-6-J7-B23


title: HctYC_OM3B_8-6-J7-A23


title: HctYC_OM3B_8-6-J7-G12


title: HctYC_OM3B_8-6-J7-A24


title: HctYC_OM3B_8-6-J7-B24


title: HctYC_OM3B_8-6-J7-B11


title: HctYC_OM3B_8-6-J7-C11


title: HctYC_OM3B_8-6-J7-C24


title: HctYC_OM3B_8-6-J7-C12


title: HctYC_OM3B_8-6-J7-A11


title: HctYC_OM3B_8-6-J7-A12


title: HctYC_OM3B_8-5-J7-P22


title: HctYC_OM3B_8-5-J7-P21


title: HctYC_OM3B_8-5-J7-O9


title: HctYC_OM3B_8-5-J7-P10


title: HctYC_OM3B_8-5-J7-O22


title: HctYC_OM3B_8-5-J7-O21


title: HctYC_OM3B_8-6-J7-D23


title: HctYC_OM3B_8-5-J7-N21


title: HctYC_OM3B_8-5-J7-N9


title: HctYC_OM3B_8-5-J7-N22


title: HctYC_OM3B_8-5-J7-M22


title: HctYC_OM3B_8-5-J7-N10


title: HctYC_OM3B_8-5-J7-M21


title: HctYC_OM3B_8-5-J7-K9


title: HctYC_OM3B_8-5-J7-O10


title: HctYC_OM3B_8-5-J7-M9


title: HctYC_OM3B_8-5-J7-L9


title: HctYC_OM3B_8-5-J7-J10


title: HctYC_OM3B_8-5-J7-J21


title: HctYC_OM3B_8-5-J7-I9


title: HctYC_OM3B_8-5-J7-L22


title: HctYC_OM3B_8-5-J7-P9


title: HctYC_OM3B_8-5-J7-I22


title: HctYC_OM3B_8-5-J7-L21


title: HctYC_OM3B_8-5-J7-L10


title: HctYC_OM3B_8-5-J7-K22


title: HctYC_OM3B_8-5-J7-K21


title: HctYC_OM3B_8-5-J7-K10


title: HctYC_OM3B_8-5-J7-J9


title: HctYC_OM3B_8-5-J7-I10


title: HctYC_OM3B_8-5-J7-J22


title: HctYC_OM3B_8-5-J7-I21


title: HctYC_OM3B_8-5-J7-H9


title: HctYC_OM3B_8-5-J7-G21


title: HctYC_OM3B_8-5-J7-F10


title: HctYC_OM3B_8-5-J7-H22


title: HctYC_OM3B_8-5-J7-H21


title: HctYC_OM3B_8-5-J7-M10


title: HctYC_OM3B_8-5-J7-H10


title: HctYC_OM3B_8-5-J7-G9


title: HctYC_OM3B_8-5-J7-E22


title: HctYC_OM3B_8-5-J7-G22


title: HctYC_OM3B_8-5-J7-D10


title: HctYC_OM3B_8-5-J7-F9


title: HctYC_OM3B_8-5-J7-C9


title: HctYC_OM3B_8-5-J7-G10


title: HctYC_OM3B_8-5-J7-E10


title: HctYC_OM3B_8-5-J7-D9


title: HctYC_OM3B_8-5-J7-F21


title: HctYC_OM3B_8-5-J7-D22


title: HctYC_OM3B_8-5-J7-E21


title: HctYC_OM3B_8-5-J7-B9


title: HctYC_OM3B_8-5-J7-D21


title: HctYC_OM3B_8-5-J7-B21


title: HctYC_OM3B_8-5-J7-B10


title: HctYC_OM3B_8-5-J7-C10


title: HctYC_OM3B_8-5-J7-C21


title: HctYC_OM3B_8-5-J7-A10


title: HctYC_OM3B_8-4-J7-P7


title: HctYC_OM3B_8-5-J7-F22


title: HctYC_OM3B_8-4-J7-P19


title: HctYC_OM3B_8-4-J7-O7


title: HctYC_OM3B_8-4-J7-P8


title: HctYC_OM3B_8-5-J7-A22


title: HctYC_OM3B_8-5-J7-B22


title: HctYC_OM3B_8-4-J7-N20


title: HctYC_OM3B_8-4-J7-N19


title: HctYC_OM3B_8-5-J7-E9


title: HctYC_OM3B_8-4-J7-P20


title: HctYC_OM3B_8-5-J7-A9


title: HctYC_OM3B_8-4-J7-O8


title: HctYC_OM3B_8-4-J7-N7


title: HctYC_OM3B_8-4-J7-O20


title: HctYC_OM3B_8-4-J7-O19


title: HctYC_OM3B_8-4-J7-M8


title: HctYC_OM3B_8-4-J7-M7


title: HctYC_OM3B_8-4-J7-M19


title: HctYC_OM3B_8-4-J7-N8


title: HctYC_OM3B_8-4-J7-L7


title: HctYC_OM3B_8-4-J7-L8


title: HctYC_OM3B_8-5-J7-A21


title: HctYC_OM3B_8-4-J7-L19


title: HctYC_OM3B_8-4-J7-K7


title: HctYC_OM3B_8-4-J7-K20


title: HctYC_OM3B_8-4-J7-J20


title: HctYC_OM3B_8-4-J7-J7


title: HctYC_OM3B_8-4-J7-J8


title: HctYC_OM3B_8-4-J7-M20


title: HctYC_OM3B_8-5-J7-C22


title: HctYC_OM3B_8-4-J7-I8


title: HctYC_OM3B_8-4-J7-I7


title: HctYC_OM3B_8-4-J7-H8


title: HctYC_OM3B_8-4-J7-H20


title: HctYC_OM3B_8-4-J7-H7


title: HctYC_OM3B_8-4-J7-I19


title: HctYC_OM3B_8-4-J7-I20


title: HctYC_OM3B_8-4-J7-L20


title: HctYC_OM3B_8-4-J7-G8


title: HctYC_OM3B_8-4-J7-G20


title: HctYC_OM3B_8-4-J7-K8


title: HctYC_OM3B_8-4-J7-F8


title: HctYC_OM3B_8-4-J7-F7


title: HctYC_OM3B_8-4-J7-G19


title: HctYC_OM3B_8-4-J7-F20


title: HctYC_OM3B_8-4-J7-K19


title: HctYC_OM3B_8-4-J7-E8


title: HctYC_OM3B_8-4-J7-F19


title: HctYC_OM3B_8-4-J7-D8


title: HctYC_OM3B_8-4-J7-E20


title: HctYC_OM3B_8-4-J7-E19


title: HctYC_OM3B_8-4-J7-E7


title: HctYC_OM3B_8-4-J7-J19


title: HctYC_OM3B_8-4-J7-D19


title: HctYC_OM3B_8-4-J7-D20


title: HctYC_OM3B_8-4-J7-C7


title: HctYC_OM3B_8-4-J7-C8


title: HctYC_OM3B_8-4-J7-C19


title: HctYC_OM3B_8-4-J7-H19


title: HctYC_OM3B_8-4-J7-G7


title: HctYC_OM3B_8-4-J7-B8


title: HctYC_OM3B_8-4-J7-B7


title: HctYC_OM3B_8-4-J7-A7


title: HctYC_OM3B_8-4-J7-C20


title: HctYC_OM3B_8-4-J7-B19


title: HctYC_OM3B_8-3-J7-P5


title: HctYC_OM3B_8-4-J7-A20


title: HctYC_OM3B_8-3-J7-P6


title: HctYC_OM3B_8-3-J7-P18


title: HctYC_OM3B_8-3-J7-P17


title: HctYC_OM3B_8-3-J7-N6


title: HctYC_OM3B_8-3-J7-O17


title: HctYC_OM3B_8-3-J7-N5


title: HctYC_OM3B_8-3-J7-O18


title: HctYC_OM3B_8-3-J7-M6


title: HctYC_OM3B_8-3-J7-N18


title: HctYC_OM3B_8-3-J7-N17


title: HctYC_OM3B_8-3-J7-M5


title: HctYC_OM3B_8-4-J7-D7


title: HctYC_OM3B_8-3-J7-M17


title: HctYC_OM3B_8-3-J7-M18


title: HctYC_OM3B_8-3-J7-L5


title: HctYC_OM3B_8-4-J7-A8


title: HctYC_OM3B_8-3-J7-K6


title: HctYC_OM3B_8-3-J7-L17


title: HctYC_OM3B_8-4-J7-A19


title: HctYC_OM3B_8-3-J7-K5


title: HctYC_OM3B_8-3-J7-L18


title: HctYC_OM3B_8-3-J7-K18


title: HctYC_OM3B_8-3-J7-O6


title: HctYC_OM3B_8-3-J7-O5


title: HctYC_OM3B_8-3-J7-J17


title: HctYC_OM3B_8-3-J7-I6


title: HctYC_OM3B_8-3-J7-I5


title: HctYC_OM3B_8-3-J7-J6


title: HctYC_OM3B_8-3-J7-J18


title: HctYC_OM3B_8-3-J7-K17


title: HctYC_OM3B_8-3-J7-J5


title: HctYC_OM3B_8-3-J7-H6


title: HctYC_OM3B_8-3-J7-H5


title: HctYC_OM3B_8-3-J7-L6


title: HctYC_OM3B_8-3-J7-H18


title: HctYC_OM3B_8-3-J7-H17


title: HctYC_OM3B_8-3-J7-I17


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title: HctYC_OM3B_6-3-J3-M5


title: HctYC_OM3B_6-3-J3-M18


title: HctYC_OM3B_6-3-J3-M17


title: HctYC_OM3B_6-3-J3-K17


title: HctYC_OM3B_6-3-J3-K6


title: HctYC_OM3B_6-3-J3-K18


title: HctYC_OM3B_6-3-J3-L18


title: HctYC_OM3B_6-3-J3-M6


title: HctYC_OM3B_6-3-J3-L5


title: HctYC_OM3B_6-3-J3-J6


title: HctYC_OM3B_6-3-J3-L17


title: HctYC_OM3B_6-3-J3-J5


title: HctYC_OM3B_6-3-J3-J18


title: HctYC_OM3B_6-3-J3-K5


title: HctYC_OM3B_6-3-J3-P17


title: HctYC_OM3B_6-3-J3-I6


title: HctYC_OM3B_6-4-J3-E20


title: HctYC_OM3B_6-3-J3-J17


title: HctYC_OM3B_6-4-J3-D19


title: HctYC_OM3B_6-3-J3-N17


title: HctYC_OM3B_6-3-J3-L6


title: HctYC_OM3B_6-3-J3-I5


title: HctYC_OM3B_6-3-J3-H6


title: HctYC_OM3B_6-3-J3-I18


title: HctYC_OM3B_6-3-J3-I17


title: HctYC_OM3B_6-3-J3-F6


title: HctYC_OM3B_6-3-J3-G5


title: HctYC_OM3B_6-3-J3-F5


title: HctYC_OM3B_6-3-J3-G6


title: HctYC_OM3B_6-3-J3-H17


title: HctYC_OM3B_6-3-J3-G18


title: HctYC_OM3B_6-3-J3-F17


title: HctYC_OM3B_6-3-J3-G17


title: HctYC_OM3B_6-3-J3-C5


title: HctYC_OM3B_6-3-J3-C17


title: HctYC_OM3B_6-3-J3-D18


title: HctYC_OM3B_6-3-J3-D5


title: HctYC_OM3B_6-3-J3-E6


title: HctYC_OM3B_6-3-J3-E18


title: HctYC_OM3B_6-3-J3-H18


title: HctYC_OM3B_6-3-J3-C6


title: HctYC_OM3B_6-3-J3-F18


title: HctYC_OM3B_6-3-J3-B5


title: HctYC_OM3B_6-3-J3-C18


title: HctYC_OM3B_6-3-J3-D6


title: HctYC_OM3B_6-3-J3-B6


title: HctYC_OM3B_6-3-J3-B18


title: HctYC_OM3B_6-3-J3-B17


title: HctYC_OM3B_6-3-J3-H5


title: HctYC_OM3B_6-2-J3-P16


title: HctYC_OM3B_6-3-J3-E17


title: HctYC_OM3B_6-3-J3-A6


title: HctYC_OM3B_6-3-J3-D17


title: HctYC_OM3B_6-3-J3-A18


title: HctYC_OM3B_6-3-J3-A17


title: HctYC_OM3B_6-2-J3-P4


title: HctYC_OM3B_6-2-J3-P3


title: HctYC_OM3B_6-2-J3-O16


title: HctYC_OM3B_6-2-J3-O4


title: HctYC_OM3B_6-2-J3-P15


title: HctYC_OM3B_6-2-J3-O3


title: HctYC_OM3B_6-2-J3-N15


title: HctYC_OM3B_6-2-J3-N16


title: HctYC_OM3B_6-2-J3-O15


title: HctYC_OM3B_6-2-J3-M16


title: HctYC_OM3B_6-2-J3-N4


title: HctYC_OM3B_6-2-J3-L15


title: HctYC_OM3B_6-2-J3-K4


title: HctYC_OM3B_6-2-J3-L16


title: HctYC_OM3B_6-3-J3-E5


title: HctYC_OM3B_6-2-J3-N3


title: HctYC_OM3B_6-2-J3-M4


title: HctYC_OM3B_6-2-J3-K15


title: HctYC_OM3B_6-2-J3-L4


title: HctYC_OM3B_6-2-J3-M15


title: HctYC_OM3B_6-2-J3-M3


title: HctYC_OM3B_6-2-J3-L3


title: HctYC_OM3B_6-2-J3-K3


title: HctYC_OM3B_6-2-J3-I3


title: HctYC_OM3B_6-2-J3-I4


title: HctYC_OM3B_6-2-J3-K16


title: HctYC_OM3B_6-2-J3-J16


title: HctYC_OM3B_6-2-J3-J3


title: HctYC_OM3B_6-2-J3-I16


title: HctYC_OM3B_6-2-J3-H3


title: HctYC_OM3B_6-2-J3-J15


title: HctYC_OM3B_6-2-J3-J4


title: HctYC_OM3B_6-2-J3-I15


title: HctYC_OM3B_6-2-J3-H16


title: HctYC_OM3B_6-2-J3-G16


title: HctYC_OM3B_6-2-J3-H15


title: HctYC_OM3B_6-2-J3-H4


title: HctYC_OM3B_6-2-J3-G3


title: HctYC_OM3B_6-3-J3-A5


title: HctYC_OM3B_6-2-J3-G15


title: HctYC_OM3B_6-2-J3-F16


title: HctYC_OM3B_6-2-J3-C15


title: HctYC_OM3B_6-2-J3-E3


title: HctYC_OM3B_6-2-J3-D3


title: HctYC_OM3B_6-2-J3-F3


title: HctYC_OM3B_6-2-J3-D15


title: HctYC_OM3B_6-2-J3-C4


title: HctYC_OM3B_6-2-J3-E16


title: HctYC_OM3B_6-2-J3-E4


title: HctYC_OM3B_6-2-J3-C16


title: HctYC_OM3B_6-2-J3-D16


title: HctYC_OM3B_6-2-J3-B4


title: HctYC_OM3B_6-2-J3-F4


title: HctYC_OM3B_6-2-J3-F15


title: HctYC_OM3B_6-2-J3-B15


title: HctYC_OM3B_6-2-J3-B3


title: HctYC_OM3B_6-2-J3-D4


title: HctYC_OM3B_6-2-J3-E15


title: HctYC_OM3B_6-2-J3-B16


title: HctYC_OM3B_6-2-J3-A4


title: HctYC_OM3B_6-2-J3-A3


title: HctYC_OM3B_6-2-J3-A16


title: HctYC_OM3B_6-2-J3-G4


title: HctYC_OM3B_6-2-J3-A15


title: HctYC_OM3B_6-1-J3-P2


title: HctYC_OM3B_6-1-J3-P1


title: HctYC_OM3B_6-1-J3-P14


title: HctYC_OM3B_6-2-J3-C3


title: HctYC_OM3B_6-1-J3-P13


title: HctYC_OM3B_6-1-J3-O2


title: HctYC_OM3B_6-1-J3-O13


title: HctYC_OM3B_6-1-J3-N13


title: HctYC_OM3B_6-1-J3-N1


title: HctYC_OM3B_6-1-J3-N14


title: HctYC_OM3B_6-1-J3-O14


title: HctYC_OM3B_6-1-J3-M14


title: HctYC_OM3B_6-1-J3-N2


title: HctYC_OM3B_6-1-J3-L13


title: HctYC_OM3B_6-1-J3-L2


title: HctYC_OM3B_6-1-J3-L14


title: HctYC_OM3B_6-1-J3-M1


title: HctYC_OM3B_6-1-J3-K1


title: HctYC_OM3B_6-1-J3-O1


title: HctYC_OM3B_6-1-J3-M2


title: HctYC_OM3B_6-1-J3-I1


title: HctYC_OM3B_6-1-J3-J2


title: HctYC_OM3B_6-1-J3-J1


title: HctYC_OM3B_6-1-J3-K13


title: HctYC_OM3B_6-1-J3-J13


title: HctYC_OM3B_6-1-J3-M13


title: HctYC_OM3B_6-1-J3-I13


title: HctYC_OM3B_6-1-J3-I2


title: HctYC_OM3B_6-1-J3-H2


title: HctYC_OM3B_6-1-J3-H1


title: HctYC_OM3B_6-1-J3-I14


title: HctYC_OM3B_6-1-J3-H14