title: KO_Female_rep3

value: nucleus ambiguus


title: EtHCYA_RNASEQ_2

status: Public on Dec 01 2024

type: SRA

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

country: China

institute: Guangxi University

library_source: transcriptomic

data_processing:
For CUT&Tag analysis, the paired-end reads were filtered and then aligned to the Eimeria tenella reference genome using Bowtie2.  The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify CUT&Tag peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
RNA-seq analysis was performed based on the reference genome of Eimeria tenella  (ToxoDB-69). Briefly, Paired-end clean reads were aligned to the reference genome using Hisat2. Read counts were calculated for each gene using the sorted bam files from htseq-count. Differentially expressed genes (DEGs) between treated and untreated parasites were calculated by edgeR. Gene expression with a fold change >4 or < -4 and p adjust < 0.01 was considered as significantly differentially expressed.
Assembly: ToxoDB-69_Eimeria tenella 2021
Supplementary files format and content: bigwig, narrowPeak

molecule: total RNA

organism: Eimeria tenella

source_name: sporozoites

growth_protocol: The E. tenella Houghton strain stably expressing Cas9 (EtHCYA) was used for the construction of knockout strain, and wild type E. tenella Houghton (EtH) strain was used for gene overexpression strain construction. These strains were maintained and propagated through one- to four-weeks-old sanhuang chickens. Chickens were reared in a coccidia-free environment and provided with water and feed free of coccidiostat and antibiotics.

extract_protocol:
For RNA-SEQ analysis, total RNAs from the sporozoites of EtHCYA and AP2-M1-KO strains were isolated using Trizol regent, and the genomic DNA was removed by DNase Ⅰ (Tiangen Biotech Co., Ltd, Beijing, China). The purity, concentration and integrity of RNAs were tested using NanoPhotometer® (IMPLEN, CA, USA), Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.  For CUT&Tag analysis, the fresh sporozoites of EtH and AP2-M1-OE strains (1×107 for each experiment) were prepared as described above. Library construction was performed by formaldehyde crosslinked CUT&Tag using the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (Novoprotein, Nanjing, China) according to the manufacturer's instructions. Briefly, fresh sporozoites were treated with 1% formaldehyde for 10 min at room temperature, and the cross-link was terminated by 1×Glycine solution. Then, the sporozoites were washed and bound to activated concanavalin A beads (10 μL/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mouse anti-Flag mAb, Abmart, Shanghai, China) at 4°C overnight. After several washes, the parasites were incubated with secondary antibody (1:100, goat anti-mouse IgG, Proteintech, USA) for 1 h at room temperature. The parasites were then resuspended with 65 μL of tagmentation Buffer (ChiTag pAG-Tn5 buffer + 1 μL of 0.7 M MgCl2) and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by 5 μL stop buffer and 1 μL proteinase K at 55°C for 2 h. DNA extraction was performed using Tagment DNA Extract Beads.
For CUT&Tag Library construction, Illumina sequencing libraries were generated by PCR amplification using specific adaptors according to the manufacturer’s recommendations (NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina B box, Novoprotein, Suzhou, China).  For RNA-seq library construction, Illumina sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Sequencing was performed using the Illumina Novaseq 6000 platform (Beijing Novogene Technology Co., Ltd) to generate 150 bp paired-end reads.

tag: tissue

value: sporozoites

tag: genotype

value: Houghton

tag: treatment

value: Cas9-expressing Eimeria tenella strain


title: KO_Female_rep6

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

country: USA

institute: Medical College of Wisconsin

data_processing:
Raw reads were demultiplexed and quality of pre-aligned data was computed by FastQC
Reads were aligned to the GRCm39 mouse reference genome with STAR 2.7.10b
Data was then further processed by featureCounts v2.0.6 to obtain read counts at the gene level
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files with raw counts for each Sample.

organism: Mus musculus

source_name: nucleus ambiguus

growth_protocol: This study was conducted using from male and female WT and Ren-aChAT-KO mice. All mice were housed in a temperature and humidity-controlled facility with ad libitum access to Teklad diet and chlorinated water.

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific).
RNA libraries were prepared using Takara low-input, SMART-seq stranded preparation kit according to manufacturer protocol

treatment_protocol: There were 4 untreated groups:WT male=6, Ren-aChAT-KO male=6, WT female=4, Ren-aChAT-KO female=6.

value: KO of Chat

value: Female


title: EtHCYA_RNASEQ_1


title: AP2_M1_KO_RNASEQ_1

value: AP2_M1 knockout strain


title: 38_S63 [Day 4, replicate 5]

city: Uppsala

first: Alma

last: Hansen

address: Ulls väg 2B

country: Sweden

institute: Statens veterinärmedicinska anstalt

description:
38_S63
Sample38

data_processing:
trimmed with Trimmomatic v0.39 using the standard Illumina adapter library, SLIDINGWINDOW:4:20 and MINLEN:50
Reads were mapped to a merged version of the reference genomes with STAR v. 2.7.2b, using default settings
Reads mapping to features were counted using HTSeq v. 0.9.1, with strandedness set on reverse, i.e. -s reverse, and otherwise default settings
Read counts loaded into R and, using edgeR, each sample was CPM normalized with regards to library size and genes filtered out that had few/no reads mapping to them across samples
Assembly: GRCg6a/pEimTen1.1
Supplementary files format and content: comma separated text files containing raw gene counts for each gene and sample, one for the chicken data and one for E. tenella

organism: Gallus gallus

source_name: Chicken caecum

extract_protocol:
TRIzol (ThermoFischer Scientific) / choloroform extraction
TruSeq stranded mRNA library preparation kit with polyA selection (Illumina) according to manufacturer’s protocol

value: Chicken caecum

value: Eimeria tenella

tag: timepoint

value: Day 4


title: ETH_CUT&Tag_2

description: CUT&Tag

library_source: genomic

data_processing:
For CUT&Tag analysis, the paired-end reads were filtered and then aligned to the Eimeria tenella reference genome using Bowtie2.  The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify CUT&Tag peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
RNA-seq analysis was performed based on the reference genome of Eimeria tenella  (ToxoDB-69). Briefly, Paired-end clean reads were aligned to the reference genome using Hisat2. Read counts were calculated for each gene using the sorted bam files from htseq-count. Differentially expressed genes (DEGs) between treated and untreated parasites were calculated by edgeR. Gene expression with a fold change >4 or < -4 and p adjust < 0.01 was considered as significantly differentially expressed.
Assembly: ToxoDB-69_Eimeria tenella 2021
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

value: wt Eimeria tenella H strain


title: AP2_M1_KO_RNASEQ_2


title: KO_Female_rep4


title: 230119-37_S1 [Day 3, replicate 2]

description:
230119-37_S1
Sample37

value: Day 3


title: 36_S70 [Day 3, replicate 4]

description:
36_S70
Sample36


title: KO_Male_rep5

value: Male


title: ETH_CUT&Tag_1

description: CUT&Tag


title: KO_Male_rep6


title: KO_Female_rep5


title: AP2_M1_CUT&Tag_2

description: CUT&Tag

value: AP2_M1 overexpression


title: 36_S57 [Day 3, replicate 4]

description:
36_S57
Sample36


title: Second relapse sample from patient, scRNA-seq

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

description:
10x Genomics
Primary cell

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using an internal pipeline. Briefly, after filtering read one without poly T tails, cell barcode and UMI was extracted. Adapters and poly A tails were trimmed (fastp V1) before aligning read two to GRCh38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2).
Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis. Cell type identification and clustering analysis using Seurat program. The Seurat program (http://satijalab.org/seurat/ , R package, v.3.0.1) was applied for analysis of RNA-Sequencing data. UMI count tables were loaded into R using read.table function. Then we set the parameter resolution to 0.6 for FindClusters function to clustering analyses.
Supplementary files format and content: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, genes.tsv, matrix.mtx).

organism: Homo sapiens

source_name: Bone marrow mononuclear cells

extract_protocol:
Mononuclear cells were isolated from bone marrow samples using lymphocyte monocyte separation medium.
ScRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X with 150 bp paired end reads.

tag: cell type

value: Bone marrow mononuclear cells

tag: diagnosis

value: AML

value: NUP98/NSD1, RUNX1/ZNF423

tag: condition

value: Second relapse


title: 35_S69 [Day 3, replicate 3]

description:
35_S69
Sample35


title: I-PDLSC_rep1

type: RNA

city: Xi‘an

first: Mei

last: Xu

address: 145th West Changle Road

institute: The Fourth Military Medical University

description: PDLSCs were cultured in medium with inflammatory cytokines

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software.

source_name: PDLSCs, inflammatory condition, 7 days

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA samples utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Total RNA of PDLSCs was extracted from the H-PDLSCs group or the I-PDLSCs group (n = 3) using TRIzol reagent (Invitrogen).

treatment_protocol: PDLSCs were cultured in normal medium (H-PDLSCs) or in medium containing inflammatory cytokines (I-PDLSCs).

value: PDLSCs

value: medium with inflammatory cytokines


title: 221228-37_S1 [Day 3, replicate 2]

description:
221228-37_S1
Sample37


title: I-PDLSC_rep2


title: Relapse sample from patient, scRNA-seq

description:
10x Genomics
Primary cell

value: Relapse


title: I-PDLSC_rep3


title: AP2_M1_CUT&Tag_1

description: CUT&Tag

value: sporozoites

value: Houghton


title: H-PDLSC_rep3

description: PDLSCs were cultured in normal medium

source_name: PDLSCs, normal condition, 7 days

value: normal medium


title: H-PDLSC_rep2

description: PDLSCs were cultured in normal medium


title: KO_Female_rep2

value: nucleus ambiguus

value: KO of Chat

value: Female


title: KO_Male_rep3


title: H-PDLSC_rep1

description: PDLSCs were cultured in normal medium


title: 33_S68 [Day 3, replicate 2]

description:
33_S68
Sample33

value: Chicken caecum

value: Eimeria tenella


title: NC

city: BEIJING

first: WEI

last: TIAN

address: FUCHENG ROAD 52#

institute: BEIJING CANCER HOSPITAL

data_processing:
Illumina Illumina HiSeq PE150  used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg38 whole genome using STAR with parameters --readFilesCommand zcat --outSAMtype BAM  SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: HCT116(colon cancer cells)

growth_protocol: The cells were seeded in Roswell Park Memorial Institute 1640 medium (RPMI 1640; GIBCO, USA), and were cultured at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA from the HCT116 cells with TTC22 overexpression or knockdown were isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq RNA Sample Preparation Kit (Illumina, USA) following TruSeq RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Purified libraries were quantified by Qubit 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq X-ten (Illumina, USA).

treatment_protocol: For overexpression of TTC22, 2ug of plasmids of pCMV-entry-TTC22 or control vetcor were transfected to about 5*10^5 HCT116 cells. For knockdown of TTC22, three siRNAs targeting TTC22 were transfected to HCT116 cells at a total contentration of 100 nM.The control group was transfected with scramble siRNA at same concentration. 48 hour later, total RNA was collected.

value: colon cancer cells

tag: cell line

value: HCT116(colon cancer cells)

value: scramble siRNA


title: KO_Male_rep1

value: Male


title: KO_Male_rep2


title: SiTTC22-123

value: three siRNAs targeting TTC22


title: M0 donor E

city: Cleveland

first: Jonathan

middle: D

last: Smith

state: OH

address: Cleveland Clinic Box ND50, 9500 Euclid Avenue

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic

data_processing:
RNAseq quality control was performed using the FastQC program.
Sequence alignments to ensembl genes were performed using STAR
Normalized counts per million (CPM), differential gene expression, and principal component analysis (PCA) was determined using DESeq2
Assembly: hg38
Supplementary files format and content: Excel spreadsheet with DESeq2 normalized CPM

source_name: iPS

growth_protocol: Human iPSC culture A. Matrigel-coated plates. 1. Thaw a tube of growth factor-reduced Matrigel on ice (Corning, # 354230) on ice 2. Add 120 l Matrigel to 12ml of DMEM/F12 (Thermo Fisher # 12500096) at 4°C (enough for 1-2 plates) and put it in ice. 3. Plate 0.5 ml mix per well in two 12-well plates (Falcon corning, # 353043, or equivalent). 4. Place plates in 37oC incubator for at least 30 min. Plates may be kept for up to 2 weeks in 37°C incubator without drying out. B. Thawing and initial plating of iPSCs. 1. iPSCs were generated by the California Institute of Regenerative Medicine and purchased from the Coriell Institute (now managed by FUJIFILM Cellular Dynamics). 2. Thaw frozen iPS vial in 37°C water bath until just thawed. Add thawed cells to 5 mL mTeSR Plus medium (Stemcell technologies, Catalog # 100-0276) in a 15 ml conical tube (Falcon corning, # 352097). Spin and wash cells with ~1 mL of mTeSR Plus medium. Spin cells and resuspend in 2 ml of mTeSR Plus medium containing 10 uM Y2763 ROCK inhibitor (Tocris, #1254).  Transfer 1 ml of cells each into two wells of the Matrigel coated 12 well plate. Place into hypoxic (5% O2) incubator. 3. Change media every day with 1 ml mTeSR+ medium (w/o Rock inhibitor). C. Passage of iPSCs by the clump culture method. 1. Ideally, cells should be growing in small clumps and reached 65–80% confluence before passage. Split at 1:3 to 1:5 every 3–4 days to avoid confluence which can lead to spontaneous loss of pluripotency. 2. Rinse cells w/ PBS, add 300 l Accutase (Gibco, # A1110501), and incubate for 5 min at 37oC. With a P1000 tip, add 1 mL of mTeSR+ w/ROCK inhibitor, and gently pipet up and down to lift cells from the plate in small clumps without dissociating into single cells. Dilute cells as needed in mTeSR+ w/ROCK inhibitor and plate cells into 3-5 wells of a Matrigel coated 12-well plate. 3. Change media every day with 1 ml mTeSR+ medium (w/o Rock inhibitor) D. Cryopreservation of iPSCs. 1. Rinse cells w/ PBS, add 300 l Accutase, and incubate for 5 min at 37oC. With a P1000 tip, add 1 mL of mTeSR+ w/ROCK inhibitor, and gently pipet up and down to lift cells from the plate in small clumps without dissociating into single cells. 2. Spin down the cells, resuspend w/ 1ml mFreSR medium (Stemcell, # 05855) containing 10 uM Rock inhibitor. 3. Transfer 1 ml cells to cryovial. Transfer vial to a slow freezing container and store at -80oC overnight, then transfer the frozen tubes to liquid nitrogen tank for long term storage. Phase 1: Embryoid body formation A. Growth of iPSCs to not more than 50% confluence on a Matrigel-coated P100 TC dish. 1. When iPSCs reach 65–80% confluence in a well of a 12 well plate, detach iPSC with Accutase as above, but pipet cells thoroughly to obtain single cell suspension. 2. Count cells and plate 7 x 10^5 cells onto a Matrigel coated P100 plate (Corning Falcon, # 353003) as described above. 3. Change to mTeSR+ medium w/o Rock inhibitor the next day. 4. About 2 days later the iPSC should not higher than 50% confluent.  Keeping the cells at this density is a critical step for successful iPSM differentiation. B. Formation of embryoid bodies in AggreWell microwell plate 1. Pre-treat one well for each iPS line in a 24-well AggreWell 800 plate (each well has 300 micropits) with 500 L Anti-Adherence Rinsing Solution (both contained in Stemcell Technologies, catalog#: 34850). 2. Centrifuge plate at 1300 x g for 5 minutes in a swinging bucket rotor fitted with plate holders. Observe plate under a microscope to ensure that bubbles have been removed from microwells. If bubbles remain trapped in any microwells, centrifuge at 1300 x g for an additional 5 minutes. 3. Aspirate Anti-Adherence Rinsing Solution from the wells. Rinse each well with 2 ml warm mTeSR Plus medium. 4. Aspirate medium from the well. Add 1 ml warm EB medium (Table 1) supplemented w/ Rock inhibitor to each well to be used. 5. Rinse 50% confluent iPSC w/ PBS and detach iPSCs with Accutase, as described above, but pipet thoroughly into single cells. Then add mTeSR Plus to quench Accutase, as above. 6. Count cells, spin down 4.5 x 10^6 IPSCs at 250 x g for 5 min. Resuspend pellet in 1 ml of EB medium supplemented w/ Rock inhibitor (10 M). 7. Add cells to well to yield achieve a final volume of: 2 mL. 8. Pipette cells up and down gently several times with P1000 pipettor to ensure even distribution. Spin plate at 100 x g for 3min. Under microscope, piled iPSCs should be observed in each microwell (Figures 1, 2). 9. Incubate the plate at 37°C in 5% O2 5% CO2 incubator. Feed with 1 ml EB medium (w/o rock inhibitor) every day for 7 days. Compact EB should be observed by day 2 (Figure 2). Phase 2: Generation of macrophage progenitors. A. Add 10 ml macrophage progenitor culture medium (Table 2) to gelatin-coated (4 ml of 0.1% gelatin incubated at 37oC for 1 hr, MP, catalog number: 901771) P100 tissue culture dish. B. Remove and discard 0.5 ml media from each well of the EB culture, yielding 1.5 ml remaining. Cut a P1000 pipet tip with sterile blade to widen the opening. Gently suspend EBs with P1000 pipet tip to dislocate each EB from the microwells. C. Transfer free EBs to a 1.5 ml sterile microfuge tube. EBs will spontaneously sediment in 1 min. Discard the supernatant and use wide open P1000 pipet tip to resuspend the EBs with progenitor culture medium.  D. Transfer resuspended EBs into previously prepared P100 tissue culture dish mentioned in step A. E. Move the P100 dish back and forth and side to side, without rotating, to evenly distribute EBs and incubate in hypoxic incubator for the first 7 days of phase 2, then move to regular incubator. Replenish with progenitor culture medium every 4 days. EBs will attach to the P100 dish and began to grow out. Harvesting macrophage progenitors. Over time, macrophage progenitors are released from the EBs and float in medium. Starting on day 29, floating progenitors in 10 ml medium may be harvested every 4 days, which are then passed through a sterile 50 m cell filter (Sysmex, #04-004-2326), to remove EB fragments, and plated onto a new gelatin coated P100 tissue culture plate. The phase 2 EBs are replenished with 10 ml progenitor culture medium. Phase 3: iPSMs maturation and maintenance Macrophage progenitors attach to the gelatin coated plates overnight and the medium is replaced with macrophage maintenance medium (Table 3).  Replenish cells with fresh maintenance medium every 4 days until usage (usually 7-10 days after harvesting progenitors).

extract_protocol:
RNA was purified using miRNeasy Kit (Qiagen, #217004) according to the manufacturer’s protocol
Oligo-dT cDNA libraries were prepared using Illumina kit
Paired end 100 bp sequencing was performed on a NovaSEQ-X instrument.

treatment_protocol: To obtain M1-like macrophages, ~ 10 days old iPSMs were incubated for 24 hrs in maintenance medium containing low dose LPS (100 ng/ml) and INF (20 ng/ml).  To obtain M2-like macrophages, ~ 10 days old iPSMs were incubated for 24hr with IL4 (20 ng/ml) in maintenance medium.

value: iPS

value: E


title: M2 donor E


title: 230119-32_S6 [Day 1, replicate 2]

description:
230119-32_S6
Sample32

value: Day 1


title: HTC116-ctrl

value: vector


title: M1 donor E


title: M2 donor D

value: D


title: KO_Male_rep4


title: NC11

city: Beijing

first: Jianqing

last: Deng

address: 6 Fucheng Road, Haidian District

department: Department of Cardiovascular Surgery

institute: The Sixth Medical Center of PLA General Hospital

data_processing:
After downloading and cleaning the reads data, we used hisat2(v2.0.5) to map the filtered reads to mouse reference genome(GRCm39), and determine its position and quantity in the genome. The mapped reads of each sample were assembled by StringTie (v1 .3.3b) (Mihaela Pertea.et al. 2015). featureCounts v1.5.0-p3 was used to count the reads numbers and then calculate FPKM of each gene.
Assembly: GRCm39
Supplementary files format and content: Supplementary_files_format_and content:ptaaexpression.csv

source_name: proximal thoracic aorta

extract_protocol:
the murine cPTAAs or sham-operated proximal thoracic aortas were harvested and stored in liquid nitrogen. Next, snap-frozen tissues were ground into powder using a mortar. A proper volume TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) was then added to the mortar, and total RNA was extracted.
the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to assess the RNA integrity. About 500ng RNA per sample underwent mRNA capture (oligo dT magnetic bead capture method), mRNA fragmentation, the first strand of cDNA synthesis using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H), the second strand of cDNA synthesis using DNA Polymerase I and RNase H, A tail and sequencing adapter addition, cDNA fragments(with sequencing adapter) screening using magnetic beads, amplification and cleaning of the library, and quality control steps.

value: proximal thoracic aorta

tag: Sex

value: male

tag: strain

value: sham surgery+normal water


title: 221228-32_S6 [Day 1, replicate 2]

description:
221228-32_S6
Sample32


title: HTC116-TTC22V1

value: overexpression TTC22V1


title: NC10


title: NC8


title: 30_S75 [Day 4, replicate 4]

description:
30_S75
Sample30

value: Day 4


title: KEC, mit ATAC, rep4

city: Paris

first: Pontoglio

last: Marco

address: 160 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades

data_processing:
1. Alignment with bowtie2 on mm10
2. Sorting reads and converting them to bams using samtools and creating index
3. Filtering bams using mm10 blackist file ENCFF547MET.bed with bedtools then indexing with samtools
4. generating bigwigs with bamCoverage, using CPM normalization
Assembly: mm10
Supplementary files format and content: bigwig

source_name: KEC

growth_protocol: Cells were grown in DMEM, 10% fetal bovine serum and 1% penicillin/streptomycin at 37C with 5% CO2.

extract_protocol:
Tagmented DNA was extracted with the MinElute PCR Purification Kit (Qiagen)
Libraries were prepared using the NEBNext Ultra II Q5 2× Master Mix (NEB) and a unique combination of i5 and i7 adapters. The appropriate number of amplification cycles was calculated analyzing an aliquote of each library by real-time PCR using the NEBNext Library Quant Kit (NEB).

treatment_protocol: Mitotic cells were obtained with a thymidine block (2mM 24h) followed by an incubation in 5uM STLC (S-trityl-L-cysteine) for 6 h

value: KEC

value: Kidney Epithelial Cell (KEC)

tag: cell cycle_stage

value: Mitosis


title: 35_S56 [Day 3, replicate 3]

description:
35_S56
Sample35

value: Chicken caecum

value: Eimeria tenella

value: Day 3


title: M1 donor D


title: 33_S55 [Day 3, replicate 2]

description:
33_S55
Sample33


title: 28_S74 [Day 4, replicate 3]

description:
28_S74
Sample28


title: NC1


title: M0 donor D


title: 28_S61 [Day 4, replicate 3]

description:
28_S61
Sample28


title: NC5


title: KEC, mit ATAC, rep3


title: KEC, mit ATAC, rep1


title: 27_S65 [Day 2, replicate 4]

description:
27_S65
Sample27

value: Day 2


title: 30_S62 [Day 4, replicate 4]

description:
30_S62
Sample30


title: cPTAA9

source_name: proximal thoracic aortic aneurysm

value: proximal thoracic aortic aneurysm

value: periaortic elatase appication and BAPN


title: 27_S52 [Day 2, replicate 4]

description:
27_S52
Sample27


title: M2 donor C

value: iPS

value: C


title: KEC, mit ATAC, rep2


title: cPTAA12


title: Progenitor donor C

value: Progenitor


title: cPTAA7


title: KEC, Asy ATAC, rep2

value: Interphase


title: 230119-22_S13 [Day 10, replicate 4]

description:
230119-22_S13
Sample22

value: Day 10


title: cPTAA6

value: male


title: M1 donor C


title: KEC, Asy ATAC, rep4


title: KEC, Asy ATAC, rep1


title: M0 donor C


title: cPTAA4


title: KEC, Asy ATAC, rep3


title: Progenitor donor B

value: B


title: cPTAA3


title: CM, LmnaFF-Myh6Cre-3 End-seq

city: Houston

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

data_processing:
FASTQC was used for the quality control check.
Peaks were called by SEACR
Diffbind was used for differential peak enrichment
Assembly: mm10 (Gencode version M25)
Supplementary files format and content: Excel file with peaks location and score
Library strategy: END-seq

source_name: Cardiac

extract_protocol:
Cardiac myocyte were isolated using the langerdoff isolation method
Illumina library construction protocol

value: Cardiac

value: Cardiac myocyte


title: 221228-22_S13 [Day 10, replicate 4]

description:
221228-22_S13
Sample22


title: 21_S103 [Day 1, replicate 1]

description:
21_S103
Sample21

value: Day 1


title: Progenitor donor A

value: A


title: cPTAA2


title: 19_S64 [Day 2, replicate 3]

description:
19_S64
Sample19

value: Chicken caecum


title: 19_S51 [Day 2, replicate 3]

description:
19_S51
Sample19

value: Eimeria tenella


title: CM, LmnaFF-Myh6Cre-1 End-seq


title: ∆eco1∆wpl1_Scc2-AID_IAA_rep2

city: Tokyo

first: Sao

middle: Anh

last: Nguyen

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: University of Tokyo

data_processing:
Raw sequencing reads were mapped to S.cerevisiae reference genomes by bwa-mem using default parameter.
Reads mapped to S.cer reference genome were qualified and filtered low quality pairs by the pairtools pipeline.
Qualified and filtered pairs were used to make contact matrix in .hic format using JuicerTool, which generate contact matrix at 5 resolutions (100, 200, 500, 1000, 2000 bp) and 4 normalizations (VC, VC_SQRT, KR and SCALE), which is ready to be visualized by the compatible web-based software Juicebox.
Loops were called by Juicer_HICCUP.
Insulation score and domains were calculated using HiCExplorer's hicFindTADs module.
Assembly: Sacharomyces Genome Database (SGD)
Supplementary files format and content: .hic format: multi-resolution contact matrix
Library strategy: Micro-C

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Budding yeast was cultured in YEPD supplemented with specific treatment as described in Method session of the manuscript.

extract_protocol:
Cells were crosslinked in 3% formaldehyde for 15 min, then quenched in 0.2M glycine for 5 min. Cells were permeabilized by 250 ug/mL Zymolyase and processed to second crosslink by 0.3M DSG for 40 min. Chromatin was fragmented by MNase at a pre-titrated concentration.
Sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Library was processed to double-sided size selection using AMPure XP Reagent (Beckman Coulter, A63881). Library was validated by Agilent High Sensitivity DNA kit and quantified by KAPA Library Quantification Kits.

tag: strain no

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 BY4741 wpl1{delta}::TRP1 eco1{delta}::LEU2 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6

value: IAA


title: iPS donor C


title: M1 donor A


title: CM, WT-3 End-seq

value: Wild type


title: M0 donor A


title: CM, WT-2 End-seq


title: ∆eco1∆wpl1_Scc2-AID_IAA_rep1


title: 18_S73 [Day 4, replicate 2]

description:
18_S73
Sample18

value: Day 4


title: 18_S60 [Day 4, replicate 2]

description:
18_S60
Sample18


title: ∆eco1∆wpl1_Scc2-AID_EtOH_rep2

value: EtOH


title: iPS donor A

value: iPS


title: iPS donor B


title: CM, WT-1 End-seq


title: 230119-17_S12 [Day 10, replicate 3]

description:
230119-17_S12
Sample17


title: ∆eco1∆wpl1_Scc2-AID_EtOH_rep1


title: RAW 264.7 cells, CPN, Day 5_3

city: Seoul

first: Heeeun

last: Woo

address: 1, Anam-dong 5(o)-ga, Seongbuk-gu

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: macrophage

value: CPN

tag: time

value: Day 5 of osteoclast differentiation


title: tobacco explants cultured with 0.5 mg/L NAA concentration Repeat 3

city: Jinzhong

first: jiagang

last: wang

address: Shanxi Agricultural University, Taigu District, Jinzhong City, Shanxi Province, China

data_processing:
Niben261_genome
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Niben261_genome .
Trimmed sequence reads were mapped to Tobacco using  Niben261_genome.
Read count extraction and normalization were performed usingNiben261_genome.
Assembly: Download the tobacco v2.6.1 version from https://solgenomics.net/
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

organism: Nicotiana tabacum

source_name: explants

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 μg 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: explants


title: tobacco explants cultured with 0.5mg/L NAA concentration Repeat 2

institute: Shanxi Agricultural University, Taigu District, Jinzhong City, Shanxi Province, China


title: CM, LmnaFF-Myh6Cre-2 End-seq


title: 221228-17_S12 [Day 10, replicate 3]

description:
221228-17_S12
Sample17

value: Day 10


title: 230119-16_S11 [Day 10, replicate 2]

description:
230119-16_S11
Sample16


title: M2 donor A


title: RAW 264.7 cells, CPN, Day 5_2


title: wt_Scc2-AID_IAA

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6


title: tobacco explants cultured with 0.5 mg/L NAA concentration Repeat 1


title: RAW 264.7 cells, CPN, Day 5_1


title: 221228-16_S11 [Day 10, replicate 2]

description:
221228-16_S11
Sample16


title: 14_S102 [Day 10, replicate 1]

description:
14_S102
Sample14


title: RAW 264.7 cells, control, Day 5_3

value: control


title: tobacco explants cultured with 0.1 mg/L NAA concentration Repeat 3


title: ∆wpl1

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1


title: RAW 264.7 cells, control, Day 5_2


title: tobacco explants cultured with 0.1mg/L NAAconcentration Repeat 2


title: 7_S101 [Day 4, replicate 1]

description:
7_S101
Sample7


title: tobacco explants cultured with 0.1 mg/L NAA concentration Repeat 1


title: Pds5-AID_IAA

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1 TIR1-9Myc:Aur1 PDS5-AID:KanMX6


title: RAW 264.7 cells, control, Day 5_1


title: 6_S100 [Day 3, replicate 1]

description:
6_S100
Sample6

value: Chicken caecum

value: Day 3


title: CmNOR_DAPseq_repeat2

first: Yongtao

last: Yu

address: 50 Zhanghua

institute: Beijing Academy of Agriculture and Forestry Sciences

description: Experimental group repeat2

data_processing:
Library strategy: DAP-seq
Reads were mapped to the Melon genome. DAP-seq peaks were called by the GEM peak caller  and ChIP-seq peaks by MACS2. Motif discovery was performed usingthe MEME-ChIP suite. Binding signals were calculated by deepTools.
Genome_build: Melon (DHL92) v3.5.1 Genome
http://cucurbitgenomics.org/ftp/genome/melon/

organism: Cucumis melo

source_name: E. coli-expressed CmNOR protein and genomic DNA of Melon

extract_protocol:
Standard His protein purification methord in E. coli
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (NEXTflex™ Rapid DNA-Seq Kit, Catalog #5144). The ampDAP-Seq DNA library was prepared by PCR amplification of a standardDAP-seq gDNA library using Phusion High-Fidelity DNA Polymerase(NEB; 15 ng of DNA in a 50 ml reaction) and the A and B adaptor oligos (REF: Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape) with the cycling conditionsbelow: 2 min at 95℃, 30 s at 98℃, 10 cycles of 15 s at 98℃, 30 s at 60℃,2 min at 72℃, and a final extension time of 10 min at 72℃, followed by a holdat 4℃. The DNA was purified by AMPure XP beads (Beckman Coulter) and resuspendedin 30 ml elution buffer. Following the DAP binding protocol, the recovered DNAwas PCR amplified for 20 cycles using the same conditions as DAP-seq usingthe full-length Illumina primers.

tag: tagged protein

value: MBP-His-CmNOR


title: Cxcr3-/- monocytes

city: Aachen

first: Zhijian

last: Li

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: RWTH Aachen University

data_processing:
ATAC-seq libraries were trimmed with Trim Galore (parameters -q 30 –paired –trim1) and aligned to mouse genome (mm10) using Bowtie2 (parameters -X2000 –no-mixed –no-discordant)
Duplicates fragments were removed, and reads were filtered for alignment quality of >Q30 using samtools
Next, we use MAC2 to perform peak calling (parameters –nomodel –nolambda –keep-dup auto –call-summits)
Transcription factor footprinting and differential activity was performed using HINT-ATAC
Genome_build: mm10

source_name: murine Cxcr3-/- bone marrow-derived cells

extract_protocol: Omni-ATAC-seq was performed according to with minor modifications. Prior to transposition dead cells were removed by centrifugation (800 rpm, 4 min, 4°C). The transposition reaction was with 7.5 μL Tagment DNA Enzyme 1 (TDE1) for 60 ‘min at 37°C. Pre-amplification was with NEBNext Ultra II Q5 Master Mix and Nextera PCR Primers (5 cycles). Quantitative PCR amplification was with NEBNext Ultra II Q5 Master Mix, Nextera PCR Primer and SYBR Gold to determine the number of additional cycles. PCR amplification of additional cycles was as for pre-amplification. PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined by Agilent High Sensitive DNA Kit and TapeStation, respectively. ATACseq libraries were sequenced on the Illumina NextSeq 500 Platform with 75 bps paired-end reads in duplicates.

tag: disease state

value: hepatocellular carcinoma (HCC)

value: monocytes


title: 3_S99 [Day 3, replicate 1]

description:
3_S99
Sample3

value: Eimeria tenella


title: CmNOR_DAPseq_repeat1

description: Experimental group repeat1

growth_protocol: Standard His protein purification methord in E. coli


title: wild type monocytes

source_name: murine wild type bone marrow-derived cells

value: wild type


title: wt_Scc2-AID_EtOH

value: EtOH


title: ∆eco1∆wpl1_rep2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 eco1{delta}::LEU2


title: ∆eco1∆wpl1_rep1


title: 2_S50 [Day 2, replicate 2]

description:
2_S50
Sample2

value: Day 2


title: 2_S63 [Day 2, replicate 2]

description:
2_S63
Sample2


title: ∆eco1∆wpl1_Scc2-PK

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 eco1{delta}::LEU2 SCC2-9PK:HIS3MX6


title: Cxcr3-/- common myeloid progenitor cells (CMP)/granulocyte-monocyte progenitor (GMP) cells

value: common myeloid progenitor (CMP), granulocyte-monocyte progenitor (GMP) cells


title: wt_rep2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: 1_S98 [Day 2, replicate 1]

description:
1_S98
Sample1


title: wt_rep1


title: HiC in P. miniata wild-type embryos at 68hpf

status: Public on Nov 30 2024

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

description: Hi-C

data_processing:
Reads from biological replicates were pooled and aligned using BWA
Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Assembly: Strongylocentrotus purpuratus 2019 Assembly (strPur5/GCF_000002235.5)
Assembly: Patiria miniata 2020 Assembly (Pmin_1.0/GCF_015706575.1)
Supplementary files format and content: multiresolution hic files

organism: Patiria miniata

source_name: whole embryo

growth_protocol: Embryos were grown at 15°C in ASW until desired developmental stage

extract_protocol:
Embryos were fixed in 2% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014, Franke et al. 2021). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for fragments between 150-600 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
End-repair, A-tailing and ligation of TruSeq indexing adapters followed standard procedure for Illumina library preparations for paired-end sequencing. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and standard TruSeq Primer 1.0 (P5) and TruSeq Primer 2.0 (P7).

value: whole embryo

value: wild-type


title: HiC in S. purpuratus wild-type embryos at 50hpf

description: Hi-C

organism: Strongylocentrotus purpuratus


title: Negative_control_repeat2

description: Negative control repeat 2

value: MBP-His


title: Pds5-AID_EtOH

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1 TIR1-9Myc:Aur1 PDS5-AID:KanMX6


title: Patient 3 PNF 003

status: Public on Nov 29 2024

city: Sacramento

first: Yongheng

last: Wang

state: CA

address: 3101 Clinical Lab Building (Research II), UC Davis Medical Center, 4625 2nd Ave.

institute: University of California Davis

description: CosMx 6000 human gene panel

hyb_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6,175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

scan_protocol: Sample processing and imaging followed NanoString's standard protocol, utilizing a pre-made 6,175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

data_processing: Data was processed using AtoMx and R.

label: Flurorescent probes (red, green, blue, yellow)

source_name: Primary nonfunction

treatment_protocol: Kidneys were collected from donors and transplanted to the recipients. Human kidney biopsies collected one hour post-transplantation.

value: Primary nonfunction allograft

tag: age

value: 51 years

value: male


title: humanized Mice#214_CD123

city: Los Angeles

first: Babak

last: Moghimi

address: 4650 sunset blvd

institute: CHLA

description:
Library name: sample4
10X genomics

data_processing:
FASTQ files generated from basecall files were demultiplexed to generate composite, filtered FASTQ files that include cell and UMI barcodes in the read headers. These files were filtered to retain only reads with the correct barcode structure, which survived Trimmomatic trimming and a low complexity filter. Cellranger (10x Genomics) was then used to aggregate the data using the `cellranger aggr` function with `normalize=mapped` (normalizing for sequencing depth) to generate a combined gene expression matrix for CD45+ human and mouse cells. The combined matrix was subsequently split to provide separate expression data for human and mouse CD45+ cells. Processed scRNA-seq data (cell-by-gene counts table) were analyzed using Seurat v5. Cells with fewer than 200 genes, fewer than 500 counts, more than 40% (human) or 35% (mouse) mitochondrial reads, or more than 30,000 UMI (human) or 50,000 UMI (mouse) were removed as low-quality. Counts were depth-normalized to a sum of 10,000 per cell and then log-transformed with a pseudo count of 1. The top 2,000 variable genes were identified, and the effects of the number of genes detected per cell were regressed out. Variable genes were defined using Seurat's `FindVariableGenes` function with the following parameters: `mean.function = ExpMean`, `dispersion.function = LogVMR`, `x.low.cutoff = 0.0125`, `x.high.cutoff = 3`, `y.cutoff = 0.5`. Cell cycle regression was performed as previously described. PCA was then performed with default settings on highly variable genes using `FindClusters` (`reduction.type = "pca"`, `dims.use = 1:10`, `resolution = 1`). Gene expression was visualized on the UMAP as log depth-normalized counts. Gene expression data were further analyzed using Partek Flow to develop biomarkers for each splenic cluster within the human and murine CD45+ populations of humanized mice. These biomarkers were input into the CellMarker algorithm (https://uncurl.cs.washington.edu/db_query) to annotate the cell clusters. For further characterization, we performed hurdle differential gene expression analysis between gated vs. constitutively expressed compartments of each collective cellular cluster, followed by Ingenuity Pathway Analysis (version 01-22-01). The outcomes were displayed as the organic view of predicted activated or inhibited cellular pathways.
Assembly: GRCh38
Supplementary files format and content: Processed data includes feature, and matrix files for individual human and mouse cells from each treated animal in .tsv, .mtx and h5 format

organism:
Homo sapiens
Mus musculus

source_name: humanized mice spleen

extract_protocol:
Tissues from the spleen of humanized mice, containing both human and mouse cells, were harvested and processed into single-cell suspensions through mechanical dissociation. Mouse and human CD45+ cells were separately enriched using CD45 nano beads and isolated via magnetic column separation. After enrichment, each population of CD45+ cells was labeled with species-specific hashing antibodies to distinguish between human and mouse cells. The labeled cells were then mixed and subjected to cell hashing using the 10X Genomics Chromium system. The cells were encapsulated, and RNA was captured for single-cell sequencing.
Single-cell RNA-Seq libraries were prepared using  the 10x Genomics Chromium Single Cell v3.2 kit

treatment_protocol: CD123 CAR-T vs CD33-CD123 CAR-T treated mice

value: humanized mice spleen

value: splenic cells

value: CD123 CAR-T


title: humanized mice#206_CD33-CD123

description:
Library name: sample2
10X genomics

value: CD33-CD123 CAR-T


title: Patient 10 IGF 010

description: CosMx 6000 human gene panel

source_name: Immediate graft function allograft

label_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6,175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

value: Immediate graft function allograft

value: 33 years

value: Female


title: humanized mice#209_CD33-CD123

description:
Library name: sample3
10X genomics


title: Patient 2 PNF 002

description: CosMx 6000 human gene panel

extract_protocol: Sample processing followed NanoString's standard protocol, utilizing a pre-made 6,175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

value: 58 years


title: humanized Mice#203_CD123

description:
Library name: sample1
10X genomics


title: humanized mice#215_CD33-CD123

description:
Library name: sample5
10X genomics


title: Patient 9 IGF 009

description: CosMx 6000 human gene panel

value: 50 years


title: Patient 8 IGF 008

description: CosMx 6000 human gene panel

value: 37 years


title: Patient 5 IGF 005

description: CosMx 6000 human gene panel

value: 36 years


title: Patient 7 IGF 007

description: CosMx 6000 human gene panel

value: 31 years

value: Male


title: Patient 6 IGF 006

description: CosMx 6000 human gene panel

value: 55 years


title: Patient 2 IGF 002

description: CosMx 6000 human gene panel


title: Patient 3 IGF 003

description: CosMx 6000 human gene panel

value: 47 years


title: Negative_control_repeat1

description: Negative control repeat 1

value: MBP-His


title: wild type common myeloid progenitor cells (CMP)/granulocyte-monocyte progenitor (GMP) cells

value: hepatocellular carcinoma (HCC)

value: wild type

value: common myeloid progenitor (CMP), granulocyte-monocyte progenitor (GMP) cells


title: Patient 4 IGF 004

description: CosMx 6000 human gene panel

value: 59 years


title: Patient 1 IGF 001

description: CosMx 6000 human gene panel

value: 42 years


title: pheS F158C_45 min

status: Public on Nov 27 2024

city: Xiamen City

first: shouqiang

last: hong

address: No. 4221-117 Xiang'an South Road

institute: Xiamen university

description: Library name: pheS F158C_phenol

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3 (Langmead, B. and S. L. Salzberg, 2012). HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected.
Assembly: Genome_build: NZ_CP009273.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Escherichia coli K-12

source_name: bacterial cultures

growth_protocol: Overnight cultures of the wildtype and pheS F158C strains were diluted 100-fold into fresh LB medium, and were grown to mid-log phase (OD600 = 0.3) at 37 °C with shaking.

extract_protocol:
Total RNAs were prepared using an RNA extraction kit following the manufacturer protocol (Tiangen, China).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, rRNAs were removed by the Ribo-zero kit to enrich mRNAs, which were then digested into short fragments. The fragmented mRNAs were used as template to generate one-strand DNA using a six-base random primer and the corresponding double-stranded cDNA. After purification, the cDNA was firstly end-repaired, A-tailed and ligated to a sequencing linker. The size of fragments was selected using AMPure XP beads. PCR amplification was performed, and the amplified products were then purified using AMPure XP beads to obtain the final library. The cDNA library was sequenced (RNA-seq) on an Illumina novaseq platform, and paired-end reads were generated.

treatment_protocol: These log-phase cultures were treated with 3.5 mg/ml phenol. After treatment for 45 min, cells were collected by centrifugation, frozen using liquid nitrogen, and then stored at -80 °C for subsequent total RNA extraction. The cultures immediately before phenol treatment were used as a control (time 0).

value: bacterial cultures

value: pheS F158C mutation

value: 3.5 mg/ml phenol for 45 min


title: pheS F158C_0 min

description: Library name: pheS F158C_None

value: No treatment


title: WT_45 min

description: Library name: WT_phenol

value: WT


title: WT_0 min

description: Library name: WT_None


title: C6_LN4

status: Public on Nov 26 2024

city: Harbin

first: Tiantongfei

last: Jiang

state: Heilongjiang

address: 黑龙江省哈尔滨市保健路157号

department: bioinformatics science and technology

institute: harbin medical university

description:
Library name: C6_LN4
10x Genomics

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 5.0.1, 10x Genomics) against the GRCh38 human reference genome. The processes were mainly performed by R package Seurat (version 4.3.0), including normalization, dimension reduction, unsupervised clustering and visualization of cell clusters. We first filtered out cells with detected genes fewer than 200 and mitochondrial gene count percentage larger than 10% (20% for the independent two patients). Then, the count matrix was normalized with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
The TDLNs were divided into two equal parts, 50% of the TDLNs samples underwent conventional diagnostic pathology procedures, while the  remaining 50% were promptly immersed in a fresh tissue-preservation solution and stored at a  temperature of -80℃.
The RNA was extracted from recently frozen tissues using the TRIzol reagent. The whole RNA's  quality was evaluated using the Bioanalyzer from Agilent Technologies. The libraries were created  by isolating total RNA and then removing ribosomal RNA using Epicentre's Ribo-Zero rRNA  Removal kit. The library was produced using 30-100 ng of Ribo-Zero RNA and the Illumina  TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA, USA). The cDNA libraries were  measured using a Qubit dsDNA HS Assay Kit and a Qubit 3.0 fluorometer (both from Thermo Fisher  Scientific, Wilmington, DE, USA) to assess their quality prior to sequencing. The RNA libraries  were subjected to sequencing using Illumina HiSeq2500 sequencers, resulting in each library  generating 2 x 50 bp paired end reads. Each lane processed two samples.

value: Lymph node

value: all cells


title: Patient 1 PNF 001

description: CosMx 6000 human gene panel

value: Primary nonfunction allograft

value: 50 years

value: male


title: C6_T

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: C6_T
10x Genomics

source_name: Colorectal cancer

value: Colorectal cancer


title: CRC3_NLN1

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: CRC3_NLN1
10x Genomics


title: CRC1_MLN1

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: CRC1_MLN1
10x Genomics


title: CRC1_T

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: CRC1_T
10x Genomics


title: CRC1_MLN2

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: CRC1_MLN2
10x Genomics


title: CRC2_NLN1

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: CRC2_NLN1
10x Genomics


title: Tissue explants from DLBC patient 08, grown for 3 days, treated with 10 mM idelalisib

city: Lausanne

first: Divyanshu

last: Srivastava

address: SV, Station 19

country: Switzerland

institute: EPFL

description: 10X Genomics Visium on FFPE samples

data_processing:
Raw sequencing reads were aligned using 10xGenomcis Space ranger pipeline (spaceranger-1.3.0).
Compressed `spatial` folder generated by spaceranger
Assembly: GRCh38
Supplementary files format and content: HDF5 format, contains gene counts for each visium spot
Supplementary files format and content: tar.gz file for the compressed `spatial` folder containing high and low res H&E images, and spot positions
Supplementary files format and content: h5ad file: Single cell reference dataset used to deconvolve Visium data
Library strategy: Spatial Transcriptomics

source_name: Lymphoid tissue explants

growth_protocol: Tumor tissue biopsies were processed with a McIlwain Tissue Chopper and placed in inserts with permeable, membranous bottom containing a 1:1 solution of Vitrogel RGD High Concentration and RPMI1640 supplemented with 5% FBS, 1x normocin, 1x insulin/selenium/transferrin, and 1x sodium pyruvate. The insert was placed in a 12 well plate and left in a 5% CO2 incubator at 37ºC for 20 minutes for the matrix to gelify. Finally, RMPI1640 complete + 0.2 micrograms/ml hBAFF was added to each well.

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) tissues were sectioned at 5 mm and placed in SuperfrostTM slides.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: Ibrutinib was added at 2 mM micromolar and idelalisib at 10 mM. Tissue explants were treated for 72h and then fixed with formalin.

value: Lymphoid tissue explants

value: DLBCL

value: Idelalisib


title: Tissue explants from DLBC patient 08, grown for 3 days, treated with 2 mM ibrutinib

description: 10X Genomics Visium on FFPE samples

value: Ibrutinib


title: Human DLBCL biopsy, patient 08

description: 10X Genomics Visium on FFPE samples

source_name: Primary lymphoid tissue

value: Primary lymphoid tissue

value: Original biopsy


title: Human ractive  lymph node biopsy, patient 03

description: 10X Genomics Visium on FFPE samples

value: reactive lymph node


title: Tissue explants from DLBC patient 08, grown for 3 days, untreated

description: 10X Genomics Visium on FFPE samples

value: Control


title: AGS, H. pylori, 24 hours, biological rep3

status: Public on Nov 25 2024

city: Nanchang

first: Leyan

state: Jiangxi

address: Donghu District

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: Sample 6
Column name in FPKMs_all_Samples.txt: AGS + H. pylori_3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: AGS

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

value: AGS

value: Human gastric adenocarcinoma cell line

tag: infection

value: H. pylori


title: AGS, biological rep3

description:
Library name: Sample 3
Column name in FPKMs_all_Samples.txt: AGS_3

value: WT

value: uninfected


title: AGS, H. pylori, 24 hours, biological rep1

description:
Library name: Sample 4
Column name in FPKMs_all_Samples.txt: AGS + H. pylori_1


title: Neurabin I+/- NPCs, rep1

city: Dubai

first: Muhammad

last: Kumail

state: Dubai

address: Al Razi road

department: CATG

country: United Arab Emirates

institute: Mohammad Bin Rashid University

description: Library name: Neurabin I+/- NPCs

data_processing:
The fast5 files generated by promethION were basecalled using Guppy. The resulting fastq files were used to produce the normalized and count matrices using epi2me-labs/wf-single-cell (https:// labs.epi2me.io/workflows/wf-single-cell/)
Assembly: GRCh38
Supplementary files format and content: Tab separated count and normalized matrices

source_name: Neural progenitor cells

extract_protocol:
Neural progenitor cells were generated from human episomal iPSC line (Thermo Fisher Scientific Cat. No.: A18945) by inducing the neural ectoderm for 7 days using neural induction media (NIM, Thermo Fisher Scientific). For this purpose, 5 x 105 cells/mL iPSCs were seeded in a six-well plate precoated with rhLaminin-521 (2.5 lg/mL concentration in DPBS with calcium, magnesium) in the presence of 10 uM Rho kinase inhibitor at 37 C in 5% CO2 incubator. The next day (day 1), the ectoderm formation was induced by replacing culture media with NIM consisting of 1x neurobasal media supplemented with 1x neural induction supplement. The spent media was replaced with fresh media every other day until day 7. On day 8, NIM was removed, and NPCs were maintained in neuronal expansion media (NEM) until 80% confluency. NEM was prepared by mixing 1x neurobasal media and 1x DMEM/F12 KO media supplemented with 0.5x neural induction supplement. NPCs were differentiated into neurons by maintaining the cells in neuronal differentiation medium (NDM) for 15 days. Briefly, after harvesting NPCs, 1 x 106 cells/mL were seeded in NEM on a culture vessel precoated with 50 lg/mL poly-Dlysine and 100 lg/mL rh-Laminin-521 in the presence of 10 lM Rho kinase inhibitor and incubated overnight at 37C in a 5% CO2 incubator. The next day (i.e., day 12), the spent NEM was replaced with fresh prewarmed NDM (1x neurobasal medium and 1x DMEM/F-12 supplemented with 1x B27 supplement, 1x N2 supplement, 10 ng/mL bFGF, and 10 mM GlutaMAX supplement). The media was changed every other day until day 22. The newly differentiated iPSC-derived neurons were used for experimental analysis after days 27?30. The data was analyzed using scRNAseq.
iPSC-derived NPCs and neurons (day 30 of differentiation) were dissociated using TrypLE Express and washed twice with PBS to remove culture media and strained using 70- lm cell strainers. Finally, the cell pellet was resuspended in PBS þ 0.04% BSA and diluted to achieve 1,200 cells/lL with a target recovery of 10,000 cells. The cell suspension was then subjected to generating barcoded single stranded cDNA molecules using a 10x chromium platform following the manufacturer?s protocol. Barcoded cDNAs (10 ng) were conjugated to Biotin tags and amplified for 13 cycles using LongAmp Hot Start Taq. Later, M280 strepta vidin beads were used to pull down the full-length bar coded cDNA molecules, followed by adapter ligation and sequencing using the PromethION system from Oxford Nanopore Technologies (Oxford, UK). For both NPCs and neurons, 50 fmol barcoded cDNA library was loaded to an independent PromethION flow cell (R10.4.1) for every sample. The average N50 of the mRNA long isoform sequencing was 900 bp

treatment_protocol: CRISPR/Cas9 editing using manufacturer's protocol

value: iPSCs-derived NPCs

value: Neural progenitor cells

value: Neurabin I+/- mutant

value: CRISPR/Cas9 editing


title: AGS, biological rep2

description:
Library name: Sample 2
Column name in FPKMs_all_Samples.txt: AGS_2


title: AGS, biological rep1

description:
Library name: Sample 1
Column name in FPKMs_all_Samples.txt: AGS_1


title: KT2440_AA, rep1

status: Public on Nov 20 2024

city: Jülich

first: Tom

last: Luthe

address: Wilhelm-Johnen-Strasse

institute: Forschungszentrum Jülich

data_processing:
CLC Genomics Workbench v 20.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the P. putida YA101 genome using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.9 similarity fraction: 0.9)
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: P. putida YA101
Supplementary files format and content: tab-delimited txt file includes TPM values for each sample

organism: Pseudomonas putida

source_name: bacterial

growth_protocol: Strains of P. putida were pre-cultured in MSM with adpic acid (AA) or 6-aminohexanoic acid (Ahx) for 16 h

extract_protocol:
RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research)
Library was constructed by Genewiz, Germany

treatment_protocol: Fresh cultures were inoculated with a starting OD600 of 0.1 and harvested after entering the mid-exponential phase

value: bacterial


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 24h, Micro-C, rep. 2

status: Public on Nov 16 2024

city: Cambridge

first: Domenic

last: Narducci

state: MA

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Assembly: mm39
*library strategy: Micro-C
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. These filtered reads were subsequently converted to .cool format using cooler (v0.9.1) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Assembly: mm39;hg38
Supplementary files format and content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions

growth_protocol: mESCs were cultured under 5% CO2 at 37°C under feeder-free conditions. The mESCs were grown in medium consisting of KnockOut DMEM (ThermoFisher #10829-018) supplemented with 15% FBS, 1000 U/mL LIF (homemade), 1 mM MEM Non-Essential Amino Acid Solution (ThermoFisher #11140050), 2 mM GlutaMAX supplement (ThermoFisher #35050061), 100 μg/mL Penicillin-Streptomycin (ThermoFisher #15140122), 0.1 mM 2-mercaptoethanol (ThermoFisher #31350010), 10 μM MEK inhibitor (Tocris #PD0325901), and 3 μM GSK inhibitor (Sigma-Aldrich #SML1046) on plates pre-coated with sterile 0.1% gelatin (Sigma-Aldrich, G1890). The mESCs were passaged every 2 days by dissociation with TrypLE Express Enzyme (ThermoFisher #12605028), and half the medium was replaced daily.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-10 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, the library pool was submitted for sequencing.

treatment_protocol: For depletion of ZFP143 in the clone A and clone B cell lines, the cells were incubated in media containing 100 μM 5-Ph-IAA (MedChemExpress #HY-134653) and 300 nM HaloPROTAC3 (Promega # GA3110), and for depletion of CTCF in the same lines the, the cells were incubated in media containing 100 nM dTAG-13 (Tocris # 6605) for 3 hours. For the depletion of ZFP143 in the clone D cell line, the cells were incubated in media containing 100 nM dTAG-13, and for the depletion of ZNF143 in the clone 30 HEK293T cell line, the cells were incubated in media containing 500 μM IAA for 3 hours.

value: Mouse embryonic stem cell

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF

value: 100nM dTAG-13

value: 24 hours


title: KT2440_AA, rep2


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 12h, Micro-C, rep. 2

value: 12 hours


title: C6_LN3

address: 黑龙江省哈尔滨市保健路157号

description:
Library name: C6_LN3
10x Genomics

tag: tissue

value: Lymph node

value: all cells


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 24h, Micro-C, rep. 1

tag: genotype


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 6h, Micro-C, rep. 2

tag: treatment

value: 6 hours


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 12h, Micro-C, rep. 1


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 6h, Micro-C, rep. 1


title: Neurabin I+/- Neurons, rep1

description: Library name: Neurabin I+/- Neurons

source_name: Neurons

value: iPSCs-derived Neurons

value: Neurons


title: JM8.N4 mESC, clone D timecourse untreated, Micro-C, rep. 1


title: Day11, scRNA

status: Public on Nov 15 2024

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

description: 10X Genomics

data_processing:
Cellranger 8.0.1
Assembly: mm10
Supplementary files format and content: loom files

source_name: Bone marrow

extract_protocol:
To perform 10X Genomics single-cell sequencing on mouse bone marrow LSK cells, begin by euthanizing the mouse following ethical guidelines and extracting the femurs and tibias. Flush the bone marrow with  PBS with 2% FBS, to obtain a single-cell suspension. Filter this suspension through a 40 µm cell strainer to remove debris and clumps. Next, enrich the LSK (Lineage^-, Sca-1^+, c-Kit^+) cells using magnetic-activated cell sorting (MACS) or fluorescence-activated cell sorting (FACS). Count the cells and assess viability using trypan blue staining or a similar method. Adjust the concentration of LSK cells to the required density, typically 700-1200 cells/µL
Load the single-cell suspension, reagents, and gel beads into the appropriate wells of a 10X Genomics Single Cell 3' Chip and run the chip in the Chromium Controller to encapsulate single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs). Perform reverse transcription within the GEMs to generate barcoded cDNA from the mRNA of individual cells, then break the emulsion and clean up the barcoded cDNA. Amplify the cDNA via PCR and assess the quality and quantity using an Agilent Bioanalyzer or similar instrument. Construct sequencing libraries from the amplified cDNA, following the 10X Genomics protocol. Sequence the libraries on  Illumina 3000 platform.

value: Bone marrow

value: LSK


title: Day8, scRNA

description: 10X Genomics


title: Day21, scRNA

description: 10X Genomics


title: AGS, H. pylori, 24 hours, biological rep2

description:
Library name: Sample 5
Column name in FPKMs_all_Samples.txt: AGS + H. pylori_2

value: AGS

value: Human gastric adenocarcinoma cell line

value: WT

value: H. pylori


title: Differentiating cells, H3K27me3 mark, sample B, 2-7 deletion

status: Public on Oct 31 2024

city: Boston

first: Frank

last: Naya

address: 24 Cummington Mall

institute: Boston University

data_processing:
Trimming adapters
Reads were aligned to to mm10 (bowtie2) and to E.coli (for spike-in normalization)
Duplicates were removed  with picard-2.8.0 and removed. Reads with a qscore<10 were removed
Files were converted to bigwig and used to compute heatmap with deeptools
Reads were normalized to their spikein using samtools with a scale factor of 1000/seq_depth and converted to the bedgraph format
Peakcalling was done using SEACR 1.3 with the stringent flag and comparing with the IgG control
Assembly: mm10
Supplementary files format and content: processd files for heatmap (bigwig), normalized reads for peakcalling (.bedgraph), peaks (.bed)
Library strategy: CUT&Run

growth_protocol: Growth: Proliferation: DMEM, 10% fetal bovine serum, 1 X penicillin/streptomycin/glutamine; Differentiation: DMEM, 2% horse serum, 1 X penicillin/streptomycin/glutamine

extract_protocol:
Extraction: Cells were collected and processed according to Epicypher CUT&RUN Protocol v2.0
Lib. con. pro.: Library prep was performed using Epicypher CUT&RUN Library Prep Kit (14-1001)

value: Inmortalized

value: 2-7 deletion

tag: cut&run antibody


title: Differentiating cells, H3K4me3 mark, sample B, 2-7 deletion

tag: cell type


title: Differentiating cells, H3K27me3 mark, sample B, 2-4 deletion

value: 2-4 deletion


title: Differentiating cells, IgG mark (control), 2-7 deletion

value: IgG


title: Differentiating cells, H3K27me3 mark, sample A, 2-4 deletion


title: Differentiating cells, H3K4me3 mark, sample B, 2-4 deletion


title: Differentiating cells, H3K4me3 mark, sample A, 2-4 deletion


title: Differentiating cells, IgG mark (control), 2-4 deletion


title: Differentiating cells, H3K27me3 mark, sample B, No deletion

value: No deletion


title: Differentiating cells, H3K27me3 mark, sample A, No deletion


title: JM8.N4 mESC, clone D timecourse untreated, Micro-C, rep. 2

value: Mouse embryonic stem cell

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF


title: Differentiating cells, H3K4me3 mark, sample A, No deletion


title: Proliferating cells, H3K27me3 mark, sample A, 2-7 deletion


title: Differentiating cells, H3K4me3 mark, sample B, No deletion


title: Proliferating cells, IgG mark (control), 2-7 deletion


title: Proliferating cells, H3K4me3 mark, sample A, 2-7 deletion


title: Differentiating cells, IgG mark (control), No deletion


title: Proliferating cells, H3K27me3 mark, sample B, 2-4 deletion


title: Day14, scRNA

description: 10X Genomics


title: Proliferating cells, H3K27me3 mark, sample A, 2-4 deletion


title: Proliferating cells, H3K27me3 mark, sample B, 2-7 deletion


title: Proliferating cells, H3K4me3 mark, sample B, 2-4 deletion


title: Proliferating cells, H3K4me3 mark, sample A, 2-4 deletion


title: Differentiating cells, H3K27me3 mark, sample A, 2-7 deletion


title: Proliferating cells, H3K4me3 mark, sample B, 2-7 deletion


title: Differentiating cells, H3K4me3 mark, sample A, 2-7 deletion


title: Proliferating cells, H3K4me3 mark, sample B, No deletion


title: Proliferating cells, H3K4me3 mark, sample A, No deletion


title: Proliferating cells, IgG mark (control), 2-4 deletion


title: Proliferating cells, H3K27me3 mark, sample A, No deletion


title: Proliferating cells, H3K27me3 mark, sample B, No deletion


title: Proliferating cells, IgG mark (control), No deletion


title: F2 fungus in Phosphate buffer (b)

status: Public on Oct 15 2024

city: Rockville

first: Helena

middle: I

last: Boshoff

state: MD

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.
The Zymo Research RNA-Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2. The pipelines was built using Nextflow. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d. BAM file filtering and indexing was carried out using SAMtools v1.9. RNAseq library quality control was implemented using RSeQC v4.0.0  and QualiMap v2.2.2-dev. Duplicate reads were marked using Picard tools v2.23.9. Reads overlapping with exons were assigned to genes using featureCounts v2.0.1.
Assembly: JAYXSC000000000
Supplementary files format and content: merged_gene_counts.txt: raw counts file

organism: Penicillium sp. F2(2024)

source_name: Fungus

growth_protocol: Fungal Mono-/ and Co-culture: Fungal biomass from axenic and co-cultures of the induced potential hits was obtained by inoculating about 300,000 spores in 4 mL Potato Dextrose Broth (PDB) media in 6 well plates (Corning Inc.) for F2/F2+Mtb; C7/C7+Mtb; F31/F31+Mtb; F50/F50+Mtb; F51/F51+Mtb. The cultures were grown at 28°C for one day. For co-cultures, 450 µL of 1X (for F2/F50/F51 fungus), 0.1X (for C7 fungus) and 0.001X (for F31 fungus) strength of Mtb freezer stock resuspended in phosphate buffer (pH 6.0) were added to fungal cultures on the next day and the cultures were incubated at 32°C at 45 rpm. All culture sets were carried out in at least two biological replicates. In contrast, fungal cultures with only phosphate buffer (pH 6.0) added were used as controls. Saturated Mtb freezer stock preparation for Co-cultures: 2 L detergent and BSA-free 7H9 media (supplemented with 4 g/L Glucose, 0.81 g/L NaCl and 0.3 g/L Casitone) was inoculated with 200 mL of wild-type Mtb H37Rv (OD600 1.0) in roller bottles and incubated at 37°C for 2 weeks. The cells were harvested by centrifuging at 4000 rpm for 30 min and were washed with 200 mL phosphate buffer saline (PBS). The cells were re-washed as above and finally resuspended in 200 mL PBS to form 10X concentrate. The cells were homogenized using glass beads (4 mm, 20 mL) by vortexing for 5 min. The 10X cell suspension was then aliquoted into cryovials and frozen at -80°C for further use. When used at different concentrations for co-culturing with fungus, the concentrated Mtb stocks were serially diluted in phosphate buffer (pH 6.0) and homogenized by using glass beads (4mm, 5 mL) for preparing a 10 mL suspension in 50 mL falcon tube followed by vortexing for at least 2 min.

extract_protocol:
Mycelia was harvested on days 6, 9 and 12 by centrifuging at 4000 rpm for 20 min followed by a brief washing with DEPC-treated water (10 mL, 4000 rpm, 20 min). The media from both mono- and co-cultures was filtered through 0.2 µm microplate filter (Millipore) from each set and validated for the growth inhibition activity against pOLYG-mScarlet Mtb H37Rv on respective days. The harvested fungal biomass was ground to fine powder in liquid nitrogen with a mortar-pestle, which was then transferred to 2-3 mL TRIzol Reagent (Invitrogen) to form a slurry and finally thawed. The samples were pipetted several times to ensure complete homogenization and were split into 2-3 RNase-free microcentrifuge tubes (1 mL each) and incubated for 5 min at RT. Chloroform (300 µL) was added to each tube and these were shaken vigorously. The samples were centrifuged at 13,000 x g at 4°C for 15 min. To the upper aqueous layer, an equal volume of 70% ethanol was added to precipitate the RNA, vortexed and the solution was loaded onto spin cartridge columns provided by PureLink RNA isolation kit (Invitrogen). Further purification steps were done according to the manufacturer’s guidelines with an on-column DNase I treatment (Zymo Research). The RNA was finally eluted in 40 μL DEPC-treated RNase-free water (Ambion, Invitrogen) and stored at -80°C. RNA concentration and purity were analyzed using Nanodrop spectrophotometer (Thermo Scientific) followed by visual assessments using Bioanalyzer (Agilent 2100) and denaturing formaldehyde agarose gel electrophoresis (1.3% agarose, formaldehyde in 1X MOPS buffer). Total RNA (at least in two biological replicates) from mono- and co-culture conditions were used for mRNA sequencing following ribosomal RNA depletion and cDNA Library prep
Libraries for mRNA sequencing were constructed at ZymoResearch from total RNA sample using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instructions. Briefly, RNA was reverse transcribed into cDNA, which was followed by ribosomal RNA depletion. After that a partial P7 adapter sequence was ligated at 3’ end of cDNAs, followed by second strand synthesis and partial P5 adapter ligation to 5’ end of the double stranded DNAs. Lastly, libraries were amplified to incorporate full length adapters under the following conditions: initial denaturation at 95°C for 10 min; 10 - 16 cycles of denaturation at 95°C for 30 sec, annealing at 60°C for 30 sec, and extension at 72°C for 60 sec; and final extension at 72°C for 7 min. Successful library construction was confirmed with Agilent’s D1000 ScreenTape Assay on TapeStation

value: Fungus

value: F2-Mtb Control


title: F2 fungus co-cultured with Mtb (b)

treatment_protocol: For co-cultures, 450 µL of 1X (for F2/F50/F51 fungus), 0.1X (for C7 fungus) and 0.001X (for F31 fungus) strength of Mtb freezer stock resuspended in phosphate buffer (pH 6.0)   were added to fungal cultures on the next day and the cultures were incubated at 32°C at 45 rpm

value: F2+0.1X Mtb


title: C7 fungus co-cultured with Mtb (b)

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.
The Zymo Research RNA-Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2. The pipelines was built using Nextflow. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d. BAM file filtering and indexing was carried out using SAMtools v1.9. RNAseq library quality control was implemented using RSeQC v4.0.0  and QualiMap v2.2.2-dev. Duplicate reads were marked using Picard tools v2.23.9. Reads overlapping with exons were assigned to genes using featureCounts v2.0.1.
Assembly: JAYXSD000000000
Supplementary files format and content: merged_gene_counts.txt: raw counts file

organism: Penicillium sp. C7(2024)


title: C7 fungus in Phosphate buffer (a)

value: C7-Mtb Control


title: C7 fungus co-cultured with Mtb (a)


title: F31 fungus co-cultured with Mtb (b)

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.
The Zymo Research RNA-Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2. The pipelines was built using Nextflow. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d. BAM file filtering and indexing was carried out using SAMtools v1.9. RNAseq library quality control was implemented using RSeQC v4.0.0  and QualiMap v2.2.2-dev. Duplicate reads were marked using Picard tools v2.23.9. Reads overlapping with exons were assigned to genes using featureCounts v2.0.1.
Assembly: JAYXSF000000000
Supplementary files format and content: merged_gene_counts.txt: raw counts file

organism: Talaromyces sp. F31


title: F31 fungus co-cultured with Mtb (a)


title: F31 fungus in Phosphate buffer (b)

value: F31-Mtb Control


title: F50 fungus co-cultured with Mtb (a)

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.
The Zymo Research RNA-Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2. The pipelines was built using Nextflow. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d. BAM file filtering and indexing was carried out using SAMtools v1.9. RNAseq library quality control was implemented using RSeQC v4.0.0  and QualiMap v2.2.2-dev. Duplicate reads were marked using Picard tools v2.23.9. Reads overlapping with exons were assigned to genes using featureCounts v2.0.1.
Assembly: JAYXSA000000000
Supplementary files format and content: merged_gene_counts.txt: raw counts file

organism: Penicillium sp. F50


title: F50 fungus co-cultured with Mtb (b)


title: F31 fungus in Phosphate buffer (a)


title: F50 fungus in Phosphate buffer (b)

value: F50-Mtb Control


title: Mtb exposed to nidulalin A containing fungal filtrate (10X MIC) for 12h rep3

data_processing:
The data was processed using the RNA-seek workflow v1.8.0 (https://doi.org/10.5281/zenodo.5223025) on the NIH HPC Biowulf cluster (http://hpc.nih.gov) with minor adaptations. References were created using the –small-genome build command.
Reads were then trimmed using cutadapt v1.18
Reads were then aligned to the NC_000962.3 reference genome using STAR v2.7.6a in 2-pass basic mode with the following adaptations to handle the small, non-intronic genome: ALIGNINTRONMAX= 1, ALIGNINTRONMIN= 0, and ALIGNMATESGAPMAX= 5000
Expression levels were quantified with RSEM v1.3.0
Assembly: NC_000962.3
Supplementary files format and content: raw counts file
Supplementary files format and content: FPKM counts file

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacterium tuberculosis H37Rv culture (10 ml) was grown to an OD600  = 0.2 in 7H9 media supplemented with 0.5% Albumin, 0.2% D-Glucose, 0.2% Glycerol, 0.085% NaCl, 0.05% Tween-80 (ADGNTw) at 37°C, 100 rpm

extract_protocol:
Cells were harvested after 6 h and 12 h exposure and were washed twice with 7H9-ADGNTw broth by centrifuging (4000 rpm, 4°C, 10 min). Cells were resuspended in 0.9 ml TRIzol and were lysed by bead beating using 0.1 mm Zr/Si beads (6000, 2-3 cycles, 30 sec; 5 mins on ice between pulses). Bead beat lysate was centrifuged (13,000 rpm, 1 min, 4°C) to remove the cell debris and 0.3 ml chloroform (Sigma) was added to the supernatant. Tubes were thoroughly shaken, allowed to sit for 5 min and centrifuged (13,000 rpm, 15 min, 4°C) to separate the upper aqueous layer. Total RNA was precipitated using equal volume of 70% ethanol and vortexed for 30 sec. The solution containing RNA was loaded onto spin cartridge columns and the RNA was eluted according to the manufacturer’s guidelines (PureLink, Invitrogen) involving on-column DNaseI treatment (Zymo Research). Total RNA was stored in aliquots at -80°C until further assessments.
About 100 ng of Total RNA was used to produce mRNA-seq samples using the Illumina TruSeq Stranded Total RNA Gold kit and sequenced as 151 bp paired-end libraries on an Illumina NextSeq 2000 P2.  cDNA prep and mRNA sequencing were done at the sequencing facility of Fredrick National Laboratory for Cancer Research (FNLCR, Fredrick, MD, USA).

treatment_protocol: Fungus and Mtb co-culture derived induced filtrates (F2+Mtb/ F31+Mtb) containing patulin  and nidulalin A were added to the Mtb cultures at 0X (Control group), 1X (Treatment 1) and 10X (Treatment 2) MIV concentrations. Control and Treatment group were done in three biological replicates each

value: F31+Mtb 10X


title: F50 fungus in Phosphate buffer (a)


title: Mtb exposed to nidulalin A containing fungal filtrate (10X MIC) for 12h rep2


title: Mtb exposed to nidulalin A containing fungal filtrate (1X MIC) for 12h rep3

value: F31+Mtb 1X


title: Mtb exposed to nidulalin A containing fungal filtrate (10X MIC) for 6h rep2


title: Mtb exposed to nidulalin A containing fungal filtrate (10X MIC) for 12h rep1


title: Mtb exposed to nidulalin A containing fungal filtrate (1X MIC) for 12h rep2


title: Mtb exposed to nidulalin A containing fungal filtrate (1X MIC) for 12h rep1


title: Mtb exposed to nidulalin A containing fungal filtrate (10X MIC) for 6h rep3


title: Mtb exposed to patulin containing fungal filtrate (10X MIC) for 12h rep2

value: F2+Mtb 10X


title: C7 fungus in Phosphate buffer (b)


title: Mtb exposed to patulin containing fungal filtrate (1X MIC) for 12h rep3

value: F2+Mtb 1X


title: Mtb exposed to patulin containing fungal filtrate (1X MIC) for 12h rep2


title: F2 fungus co-cultured with Mtb (a)


title: F2 fungus in Phosphate buffer (a)


title: Mtb exposed to nidulalin A containing fungal filtrate (1X MIC) for 6h rep2


title: Mtb exposed to nidulalin A containing fungal filtrate (1X MIC) for 6h rep1


title: Mtb exposed to nidulalin A containing fungal filtrate (1X MIC) for 6h rep3


title: Mtb exposed to patulin containing fungal filtrate (10X MIC) for 6h rep2


title: Mtb exposed to nidulalin A containing fungal filtrate (10X MIC) for 6h rep1


title: Mtb exposed to patulin containing fungal filtrate (10X MIC) for 12h rep3


title: Mtb exposed to patulin containing fungal filtrate (1X MIC) for 12h rep1


title: Mtb exposed to patulin containing fungal filtrate (1X MIC) for 6h rep2


title: Mtb exposed to patulin containing fungal filtrate (10X MIC) for 6h rep1


title: Mtb exposed to patulin containing fungal filtrate (10X MIC) for 12h rep1


title: Mtb untreated 6h control rep2

value: Control


title: Mtb untreated 12h control rep1


title: Mtb exposed to patulin containing fungal filtrate (1X MIC) for 6h rep3


title: Mtb untreated 12h control rep3


title: Mtb untreated 12h control rep2


title: Mtb untreated 6h control rep3


title: F51 fungus co-cultured with Mtb (a)

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq 6000 to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.
The Zymo Research RNA-Seq pipeline was originally adapted from nf-core/rnaseq pipeline v1.4.2. The pipelines was built using Nextflow. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. Trimmed reads were aligned to the reference genome using STAR v2.6.1d. BAM file filtering and indexing was carried out using SAMtools v1.9. RNAseq library quality control was implemented using RSeQC v4.0.0  and QualiMap v2.2.2-dev. Duplicate reads were marked using Picard tools v2.23.9. Reads overlapping with exons were assigned to genes using featureCounts v2.0.1.
Assembly: JAYXSB000000000
Supplementary files format and content: merged_gene_counts.txt: raw counts file

organism: Penicillium sp. F51


title: F51 fungus in Phosphate buffer (b)

value: F51-Mtb Control


title: F51 fungus co-cultured with Mtb (b)


title: Exon 23, part 2, none, replicate 2

status: Public on Sep 27 2024

city: Frederick

first: Shyam

last: Sharan

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

data_processing:
The reads were demultiplexed using bcl2fastq
SeqPrep was used for adapter trimming and merging the read pairs
The reads were aligned to GRCh38 reference genome using the needleall command from the EMBOSS package
Gaussian mixture-model was applied to HDR counts to get function score
Assembly: GRCh38
Supplementary files format and content: SNV function scores and classification

organism: Mus musculus

growth_protocol: Mouse embryonic stem cell line expressing a single copy of human BRCA2 [Clone: F7/F7] was cultured with underlying feeder cells (SNLP) that express leukemia inhibitory factor (Lif) and puromycin and neomycin resistance cassettes. The maintenance medium consisted of Knockout DMEM (Gibco) supplemented with 15% FBS (HyClone), penicillin-streptomycin-glutamine (Gibco) and 0.1 mM b-mercaptoethanol. The media was changed every day and cells were trypsinized when ESCs reached 80% confluency.

extract_protocol:
Genomic DNA was extracted from the cell pellets utilizing the Zymo Genomic DNA Extraction kit
The DNA libraries were prepared in line with the protocol specified in the Illumina TruSeq Nano DNA Library Prep kit

value: Embryonic stem cell

tag: time point

value: Day 3

tag: exon

tag: part

tag: replicate


title: F51 fungus in Phosphate buffer (a)


title: Exon 23, part 2, none, replicate 1

tag: cell line


title: Mtb untreated 6h control rep1


title: Exon 23, part 2, olaparib, replicate 2

value: olaparib

value: Day 14


title: Mtb exposed to patulin containing fungal filtrate (10X MIC) for 6h rep3


title: Exon 23, part 2, olaparib, replicate 1


title: Exon 23, part 2, DMSO, replicate 2

value: DMSO


title: Exon 20, part 1, none, replicate 2


title: Exon 23, part 2, cisplatin, replicate 2

value: cisplatin


title: Exon 23, part 2, cisplatin, replicate 1


title: Exon 20, part 1, olaparib, replicate 1


title: Exon 23, part 2, DMSO, replicate 1


title: Mtb exposed to patulin containing fungal filtrate (1X MIC) for 6h rep1


title: Exon 20, part 1, olaparib, replicate 2


title: Exon 20, part 1, DMSO, replicate 2


title: Exon 20, part 1, none, replicate 1


title: Exon 20, part 1, cisplatin, replicate 2


title: Exon 20, part 1, DMSO, replicate 1


title: Exon 20, part 1, cisplatin, replicate 1


title: Exon 16, part 1b, none, replicate 2


title: Exon 16, part 1b, olaparib, replicate 1


title: Exon 16, part 1b, olaparib, replicate 2


title: Exon 16, part 1b, DMSO, replicate 2


title: Exon 16, part 1b, DMSO, replicate 1


title: Exon 16, part 1b, cisplatin, replicate 2


title: Exon 16, part 1b, cisplatin, replicate 1


title: Exon 16, part 1a, none, replicate 1


title: Exon 16, part 1a, olaparib, replicate 1


title: Exon 16, part 1a, DMSO, replicate 1


title: Exon 16, part 1a, none, replicate 2


title: Exon 16, part 1a, olaparib, replicate 2


title: Exon 16, part 1a, cisplatin, replicate 2


title: Exon 16, part 1a, cisplatin, replicate 1


title: Exon 16, part 1b, none, replicate 1


title: Exon 26, part 2, none, replicate 2

data_processing:
The reads were demultiplexed using bcl2fastq
SeqPrep was used for adapter trimming and merging the read pairs
The reads were aligned to GRCh38 reference genome using the needleall command from the EMBOSS package
Gaussian mixture-model was applied to HDR counts to get function score
Assembly: GRCh38
Supplementary files format and content: SNV function scores

value: expressing a single copy of human BRCA2 [Clone:F7/F7]


title: Exon 26, part 2, DMSO, replicate 1


title: Exon 26, part 2, DMSO, replicate 2


title: Exon 26, part 2, none, replicate 1


title: Exon 26, part 1, none, replicate 2


title: Exon 26, part 2, cisplatin, replicate 2


title: Exon 26, part 2, olaparib, replicate 1


title: Exon 26, part 2, cisplatin, replicate 1


title: Exon 26, part 2, olaparib, replicate 2


title: Exon 26, part 1, DMSO, replicate 1


title: Exon 26, part 1, cisplatin, replicate 2


title: Exon 26, part 1, DMSO, replicate 2


title: Exon 26, part 1, olaparib, replicate 2


title: Exon 26, part 1, olaparib, replicate 1


title: Exon 26, part 1, cisplatin, replicate 1


title: Exon 16, part 1a, DMSO, replicate 2


title: Exon 25, part 7, none, replicate 2


title: Exon 25, part 7, DMSO, replicate 2


title: Exon 25, part 6, none, replicate 1


title: Exon 25, part 6, none, replicate 2


title: Exon 25, part 7, cisplatin, replicate 2


title: Exon 25, part 6, olaparib, replicate 1


title: Exon 25, part 7, cisplatin, replicate 1


title: Exon 25, part 6, olaparib, replicate 2


title: Exon 25, part 6, DMSO, replicate 2


title: Exon 25, part 6, DMSO, replicate 1


title: Exon 26, part 1, none, replicate 1


title: Exon 25, part 6, cisplatin, replicate 2


title: Exon 25, part 6, cisplatin, replicate 1


title: Exon 25, part 5, DMSO, replicate 2


title: Exon 25, part 7, none, replicate 1


title: Exon 25, part 5, DMSO, replicate 1


title: Exon 25, part 5, olaparib, replicate 1


title: Exon 25, part 5, cisplatin, replicate 1


title: Exon 25, part 4, none, replicate 2


title: Exon 25, part 4, olaparib, replicate 1


title: Exon 25, part 5, none, replicate 2


title: Exon 25, part 4, DMSO, replicate 2


title: Exon 25, part 4, DMSO, replicate 1


title: Exon 25, part 4, cisplatin, replicate 2


title: Exon 25, part 5, cisplatin, replicate 2


title: Exon 25, part 4, cisplatin, replicate 1


title: Exon 25, part 3, none, replicate 2


title: Exon 25, part 3, none, replicate 1


title: Exon 25, part 3, olaparib, replicate 1


title: Exon 25, part 3, olaparib, replicate 2


title: Exon 25, part 3, cisplatin, replicate 2


title: Exon 25, part 3, DMSO, replicate 2


title: Exon 25, part 3, cisplatin, replicate 1


title: Exon 25, part 3, DMSO, replicate 1


title: Exon 25, part 2, none, replicate 2


title: Exon 25, part 2, none, replicate 1


title: Exon 25, part 5, olaparib, replicate 2


title: Exon 25, part 2, olaparib, replicate 2


title: Exon 25, part 5, none, replicate 1


title: Exon 25, part 2, olaparib, replicate 1


title: Exon 25, part 2, DMSO, replicate 2


title: Exon 25, part 2, DMSO, replicate 1


title: Exon 25, part 1, none, replicate 1


title: Exon 25, part 1, DMSO, replicate 2


title: Exon 25, part 1, none, replicate 2


title: Exon 25, part 1, olaparib, replicate 2


title: Exon 25, part 4, none, replicate 1


title: Exon 25, part 2, cisplatin, replicate 1


title: Exon 25, part 1, DMSO, replicate 1


title: Exon 25, part 7, DMSO, replicate 1


title: Exon 25, part 2, cisplatin, replicate 2


title: Exon 25, part 1, olaparib, replicate 1


title: Exon 25, part 1, cisplatin, replicate 1


title: Exon 24, part 3, none, replicate 2


title: Exon 25, part 1, cisplatin, replicate 2


title: Exon 24, part 3, DMSO, replicate 2


title: Exon 24, part 3, olaparib, replicate 1


title: Exon 24, part 3, none, replicate 1


title: Exon 24, part 3, olaparib, replicate 2


title: Exon 24, part 3, cisplatin, replicate 2


title: Exon 24, part 3, DMSO, replicate 1


title: Exon 24, part 2, olaparib, replicate 2


title: Exon 24, part 3, cisplatin, replicate 1


title: Exon 24, part 2, none, replicate 2


title: Exon 24, part 2, DMSO, replicate 2


title: Exon 23, part 3, none, replicate 1


title: Exon 24, part 1, DMSO, replicate 2


title: Exon 24, part 2, olaparib, replicate 1


title: Exon 23, part 3, olaparib, replicate 2


title: Exon 24, part 2, none, replicate 1


title: Exon 24, part 2, cisplatin, replicate 1


title: Exon 24, part 1, olaparib, replicate 2


title: Exon 24, part 1, DMSO, replicate 1


title: Exon 23, part 3, cisplatin, replicate 2


title: Exon 23, part 3, cisplatin, replicate 1


title: Exon 23, part 3, olaparib, replicate 1


title: Exon 24, part 1, none, replicate 1


title: Exon 23, part 1, none, replicate 2


title: Exon 23, part 1, none, replicate 1


title: Exon 23, part 1, olaparib, replicate 2


title: Exon 23, part 1, olaparib, replicate 1


title: Exon 23, part 3, DMSO, replicate 1


title: Exon 24, part 1, cisplatin, replicate 2


title: Exon 24, part 2, DMSO, replicate 1


title: Exon 24, part 1, none, replicate 2


title: Exon 24, part 2, cisplatin, replicate 2


title: Exon 24, part 1, olaparib, replicate 1


title: Exon 23, part 3, none, replicate 2


title: Exon 24, part 1, cisplatin, replicate 1


title: Exon 23, part 1, DMSO, replicate 1


title: Exon 23, part 1, DMSO, replicate 2


title: Exon 22, part 4, none, replicate 2


title: Exon 23, part 1, cisplatin, replicate 1


title: Exon 23, part 1, cisplatin, replicate 2


title: Exon 22, part 4, none, replicate 1


title: Exon 22, part 4, olaparib, replicate 1


title: Exon 22, part 4, olaparib, replicate 2


title: Exon 22, part 4, DMSO, replicate 2


title: Exon 22, part 3, olaparib, replicate 2


title: Exon 22, part 4, DMSO, replicate 1


title: Exon 22, part 3, none, replicate 1


title: Exon 22, part 3, cisplatin, replicate 2


title: Exon 22, part 4, cisplatin, replicate 1


title: Exon 22, part 2, none, replicate 2


title: Exon 22, part 2, olaparib, replicate 2


title: Exon 22, part 3, DMSO, replicate 1


title: Exon 22, part 2, olaparib, replicate 1


title: Exon 22, part 3, olaparib, replicate 1


title: Exon 22, part 3, cisplatin, replicate 1


title: Exon 22, part 2, DMSO, replicate 2


title: Exon 22, part 3, none, replicate 2


title: Exon 22, part 2, none, replicate 1


title: Exon 22, part 2, DMSO, replicate 1


title: Exon 22, part 1, none, replicate 2


title: Exon 22, part 2, cisplatin, replicate 2


title: Exon 22, part 1, none, replicate 1