title: STAMP_09

extract_protocol: To confirm the RNA quality of all the samples included in this study three consecutive 10-μm scrolls for the isolation and purification of total RNA using the Norgen Biotek FFPE RNA Purification Kit (Product ID 25300). RNA material (5 ng) was analyzed using a 5200 Fragment Analyzer with the High Sensitivity RNA Assay kit (DNF-472, Agilent Technologies). DV200 values across all samples ranged between 50%–70%. Single Nucleus RNA sequencing was performed following the snPATHO-Seq protocol (Wang et al. BioRxiv, 2023). Briefly, two 30- to 50-μm-thick scrolls from each sample, adjacent to sections for CosMx, Xenium, and H&E staining, were cut and placed into 1.5-mL Eppendorf tubes and stored at 4°C inside Ziplock bags with desiccants to control moisture. Scrolls were stored for up to 1 week. For the preparation of nuclei suspensions, scrolls sections underwent a triple wash in 1 mL of xylene (214736, Millipore Sigma) for 10 minutes each to dewax, followed by rehydration through sequential ethanol (E7023, Millipore Sigma) immersions of decreasing concentrations (100% twice, then 70%, 50%, and 30% once each), each for a duration of 1 minute. Of note, the initial xylene wash was performed at 55°C for 10 minutes to enhance paraffin removal. Subsequent to rehydration, a single wash was performed using 1 mL of wash RPMI 1640 media (11875093, Gibco). After removing the RPMI1640 wash, 50–100 uL of digestion mix [RPMI1640 supplemented with 1 mg/mL of Liberase TH (5401151001, Millipore-Sigma), along with 1 U/uL RNAse Inhibitor (RiboLock RNase Inhibitor, EO0382, Thermo Fisher Scientific)] was added to the tissue scrolls breaking them to smaller pieces with a 1.5-mL pellet pestle before topping up to 1 mL with the same digestion media. Digestion was carried out in a Thermomixer at 800 rpm. After digestion, 400 uL of Ez Lysis Buffer (NUC-101, Sigma-Aldrich) was added, mixed by inversion five times, and centrifuged at 850xRCF for 5 minutes at 4°C. The pellet, consisting of released nuclei and undigested tissue, was resuspended in 250 uL of Ez Lysis buffer with 2% BSA (130-091-376,  MACS BSA Stock Solution, Miltenyi) and 1 U/uL RNAse Inhibitor, followed by homogenization using a 1.5-mL pellet pestle. This was supplemented with an additional 750 uL of the same lysis mix, with further disaggregation achieved through pipetting. The sample was then filtered through a 70-μm strainer (pluriStrainer Mini 70um, 43-10070-50, pluriSelect) and centrifuged, with the flow-through washed again with 800 uL of the lysis mix. Nuclei pellet was washed three times in 1x PBS (70011044, Gibco) with 1% BSA, followed by two washes in 0.5x PBS (70011044, Gibco) with 0.02% BSA. Nuclei was finally resuspended in a volume of 500-1000 uL of the same buffer, dependent on pellet size, and filtered through a 40-μm strainer (pluriStrainer Mini 40um, 43-10040-50, pluriSelect. Nuclei were counted using a Luna-FX7 using Acridine Orange/Propidium Iodide Stain (Logos). For immediate analysis, the suspension was kept on wet ice until processing using the Chromium X controller and the Chromium Fixed RNA Profiling Reagent Kits for multiplexed samples (Chromium Fixed RNA Kit, Human Transcriptome, PN1000475; Chromium Next GEM Chip Q Single Cell Kit, PN-1000418; Dual Index Kit TS Set A, PN-1000251, 10x Genomics) and the User guide CG000527, Rev E. For storage, the pre- or post-hybridized nuclei suspensions were supplemented with 10% Glycerol and 0.1X Enhancer (PN-2000482, 10x Genomics), rested on ice for 10 minutes, and then cryopreserved at −80°C. For the hybridization step, between 500,000 and 1.5 million nuclei were used; hybridization was conducted for 20 hours at 42°C across all samples. BC1-4 were used in all samples used in this study. Post-hybridization washes were carried out in a pool-wash setting as per User guide, with an additional wash included. Approximately 10,000 nuclei/sample were aimed for capture. An extra cycle was introduced for the Pre-Amplification PCR step. Indexing PCR conditions were tailored to attain the target library concentration of 50–200 nM. Libraries were checked for quality control and quantified using a Fragment Analyzer 5200 (Agilent) and a Qbit Flex Fluorometer (Thermo Fisher Scientific), respectively. The indexed libraries were sequenced using the Illumina NovaSeq 6000 system. The read configuration was Read 1: 28, i7: 10, i5: 10, and Read 2: 90. Libraries were sequenced to aim for 20,000–30,000 read pairs/nuclei.

value: Single Molecule Imager

value: CosMx Human Universal Cell Characterization RNA Panel:1000


title: Medalist trial patient Responderj1376_samp4

status: Public on Jun 23 2025

type: SRA

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

country: USA

institute: Einstein College of Medicine

description: Library name: j1376_samp4

library_source: transcriptomic

data_processing:
RNA seq read mapping, differential expression analysis, and splicing analysis:  We used HISAT2 2.0.0-beta to align readings with GRCh38. The htseq-count tool was used to find the total number of read pairs that were uniquely mapped. We have made the data accessible through the NCBI's Gene Expression Omnibus (GEO) repository. To identify transcripts undergoing alternative splicing (AS) events between conditions, we utilized the rMATS (Robust Multi-array Average Transcript Splicing) tool. This tool was employed to detect various AS events, such as skipped exons, alternative 5' or 3' splice sites, and retained introns. The inclusion level (percent spliced-in, PSI) for each splicing event across samples was calculated. Using rMATS, a statistical model was applied to pinpoint AS events showing significant changes in PSI between conditions. Differentially spliced events were identified based on a user-defined fold-change threshold for PSI alteration and an adjusted p-value threshold for statistical significance.
Reads were aligned to the reference with tophat2 using the “-g 1” parameter setting.
Gene expression was enumerated with htseq2 using gencode.v24.primary_assembly
Assembly: GRCh38_no_alt_analysis (hg38)
Supplementary files format and content: tab delimited txt file with Ensembl identifier and count columns

molecule: total RNA

organism: Homo sapiens

source_name: Medalist trial patient Responder

growth_protocol: Cells were cultured in IMDM, 15% FBS, 15% human serum, 1% penicillin/steptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA library preparation:  The RNA quality was analyzed using a bioanalyzer. RNA samples with RQN scores above an 8 were considered suitable for RNA library preparation. The library preparation process followed the manufacturer's protocol (QIAseq Stranded RNA Lib Kit UDI-B, Cat# 180452). Initially, RNA molecules were fragmented into smaller fragments, and then reverse transcriptase was used to convert the fragmented RNA into double-stranded cDNA. Adaptor ligation was performed, followed by library amplification to ensure sufficient cDNA fragments for sequencing. Prior to sequencing, the library underwent quality control and quantification. Sequencing was conducted using an Illumina sequencer (Nextseq500) with 150 paired-end sequencing, resulting in the generation of approximately 30 million reads per sample.
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA was eluted in RNAse free water. At least 0.5 ug of total RNA was used to prepare libraries.
QIAseq Stranded RNA Lib Kit UDI (24) Cat no. / ID.  180450

treatment_protocol: Cells were either treated with GDF11 (100 ng/mL) or TGFb1 (20 ng/mL)

tag: cell type

value: BMMNCs

tag: treatment

value: Luspatercept


title: Siberian hamster, Amygdala, Long Photoperiod, Sample 5

city: Glasgow

first: Tyler

last: Stevenson

address: Jarret Building

department: School of Biodiversity, One Health, and Comparative Medicine

country: United Kingdom

institute: University of Glasgow

description: Library name: Hamster Am 238

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25bp reads)
Minimap2 used to align reads to either Mus musculus (GRCm39) or Coturnix japonica (2.0) genome
Transcript expression levels generated using Salmon
Assembly: GCF_000001635.27 (Mus musculus) or GCF_001577835.1 (Coturnix japonica)
Supplementary files format and content: Comma Separated Values Files with expressed gene transcripts for each sample

molecule: polyA RNA

organism: Phodopus sungorus

source_name: Amygdala

extract_protocol:
RNA was extracted using TRIzol reagent according to manufacturer instructions and cleaned using a Qiagen RNEasy MinElute Cleanup Kit
RNA was processed into cDNA libraries using the SQK PCB 111.24 cDNA Barcoding Kit (Oxford Nanopore Technologies) according to manufacturer instructions

tag: tissue

value: Amygdala

value: Long 16L Photoperiod


title: WJL4185_RLF_N034

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

description:
Library name: WJL4185
Jkappa1 coding end bait

library_source: genomic

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2. The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

molecule: genomic DNA

organism: Mus musculus

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h.

tag: cell line

value: vAbl-ProB

value: pro-B cells

tag: genotype

value: p53-/- Setx deletion exon 3


title: Medalist trial patient Responderj1376_samp6

description: Library name: j1376_samp6


title: STAMP_13

type: RNA

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

hyb_protocol: The Imaging based platforms used in this study are the CosMX SMI (Nanostring) and the Xenium Analyzer (10X Genomics) with all specifications required for this study outlined in the CosMX SMI was used for both RNA and protein assays. All sections were also stained after data acquisition on their respective imaging platform. The specifics for each assay is outlined in the proceeding sections and found in STSOP. All methods were used across the three institutions: site #1 (UoA), site #2 (St. Jude Children’s Research Hospital), and site #3 (Weill-Cornell Medicine).  CosMx RNA Slide Preparation: Samples were processed following the guidelines outlined in the CosMx slide preparation manual MAN-10159-02 for prostate cancer processed in Adelaide and MAN-10184-01-1 for all other tissues. In summary, 5-μm sections were placed onto the 15 mm x 22 mm scannable area of a Superfrost Plus Micro Slide (VWR, 48311-703) and dried in an oven at 37°C for 2 hours then kept at room temperature with desiccant overnight before storage at 4°C. The slides were then incubated overnight at 60°C for 17–18 hours and then brought to room temperature for 3–5 minutes. This was followed by two xylene washes for 5 minutes each, and two washes in 100% ethanol for 2 minutes each. For normal tissues, CitroSolv workflow was used in place of xylene. The slides were then dried in an oven at 60°C for 5 minutes. The slides were immersed in pre-heated 1X Target Retrieval solution (CosMx FFPE slide preparation kit, RNA) in a pressure cooker (or steamer) at 100°C for 15 minutes, timing started once the retrieval solution reached 100°C. The slides were immediately transferred to water for 15 seconds, then washed in 100% ethanol for 3 minutes, and air-dried at room temperature for 30 minutes to 1 hour. Incubation frames were attached to each slide, and a pre-warmed digestion buffer containing 3 ug/mL Proteinase K (CosMx FFPE slide preparation kit, RNA) and 1X PBS (AM9922, AM9625 was applied and incubated in a hybridization chamber for 30 minutes. The slides were then rinsed twice in water, and fiducials were applied at 0.001%, followed by a 5-minute incubation at room temperature, shielded from light. The slides underwent a 1X PBS wash for 1 minute, were fixed in 10% NBF for 1 minute, immediately followed by two washes in NBF stop buffer for 5 minutes each, and then a 5-minute wash in 1X PBS. A 100 mM NHS-acetate solution was applied to the tissue for 15 minutes at room temperature, followed by two washes in 2X SSC for 5 minutes each. The CosMx Human Universal Cell Characterization RNA Panel (CMX-H-USCP-1KP-R) targeting 950 human genes and a 50-target add-on panel set, were denatured at 95°C for 2 minutes and then cooled on ice for 1 minute. A probe mix containing RNase inhibitor, buffer R, and nuclease free water was applied to the slide and incubated for 17 hours in the hybridization chamber at 37°C. Post-incubation, the slides were washed twice in a final concentration of 50% deionized formamide and 2X SSC mix for 25 minutes each, followed by two washes in 2X SSC for 2 minutes each. DAPI stock was diluted to 1:40 and applied to the slides for 15 minutes at room temperature, protected from light. The slides were then washed in 1X PBS for 5 minutes and stained for 1 hour with a cocktail of CD298/B2M, PanCK, CD45, and CD68 antibodies (Item # 121500020, 121500021, 121500022). Colon, HCC TMA, pancreas, and prostate cancer samples were stained with 4 uL of the CD298/B2M antibody, following the guidelines in MAN-10184-01-1. In contrast, appendix, ileum, and prostate cancer samples received a staining of 8 uL of the CD298/B2M antibody, as specified in MAN-10159-01-1.The slides were washed three times in 1X PBS for 5 minutes each and then stored in 2X SSC. The pre-bleaching profile followed configuration C, while the cell segmentation profile adhered to configuration A, except for the HCC TMA, which used configuration E. These procedures were consistently applied across all sites: St. Jude Children's Research Hospital, Weill Cornell Medical Center, and the University of Adelaide, with FOVs remaining uniform across all three locations.  CosMx Protein Slide Preparation: Samples were processed according to the guidelines provided in the CosMx SMI slide preparation manual MAN-10185-01-1 (NanoString). In summary, 5-μm FFPE sections were placed onto the 15 mm x 22 mm scannable area of a Superfrost Plus Micro Slide and dried in an oven at 37°C for 12 hours, sealed with desiccant and dried for a further 12 hours at room temperature before storage at 4°C. The slides were baked at 65°C for 2 hours and then equilibrated to room temperature for 3–5 minutes, and then washed twice in xylene (or CitriSolv) for 5 minutes each at room temperature. The slides were then washed twice in 100% ethanol for 10 minutes each, twice in 95% ethanol for 5 minutes each, and once in 70% ethanol for 5 minutes, followed by two washes in 1X PBS for 5 minutes each. The slides were immersed in pre-heated 1X Target Retrieval solution and heated in a pressure cooker at 100°C with the valve closed for 15 minutes, then allowed to equilibrate to room temperature in the same solution. Afterward, the slides were washed three times in 1X PBS for 5 minutes each, and incubation frames were attached. Tissue sections were then covered with Buffer W and incubated at room temperature for 1 hour in the dark. The NanoString 64-plex human protein antibody panel was combined with CD298/B2M and PanCK/CD45 segmentation markers in Buffer W. Samples from the appendix, ileum, and pancreas were also incubated with the CD68 segmentation marker. The primary antibody mix was incubated at 4°C for 17 hours, followed by three washes with 1X TBS-T buffer for 10 minutes each and once with 1X PBS for 2 minutes. Fiducials, prepared at the recommended concentration of 0.00005%, were applied to the slides at room temperature for 5 minutes, protected from light. Slides were then washed once with 1X PBS for 5 minutes and fixed with 4% PFA for 15 minutes. This was followed by three washes in 1X PBS for 5 minutes each. Sections were stained with nuclei stain for 10 minutes, washed twice with 1X PBS for 5 minutes, and incubated with 100 mM NHS acetate for 5 minutes, before a final wash in 1X PBS for 5 minutes. The selected pre-bleaching profile was configuration C, and the cell segmentation profile was configuration A. These procedures were uniformly followed at St. Jude Children's Research Hospital, Weill Cornell Medical Center, and the UoA, ensuring consistency in the FOVs across all three locations. Breast cancer, normal appendix, and normal ileum samples processed as part of the NanoString’s Technology Access Program followed the methods previously described (He et al,. Nat Biotechnol, 2022).  Xenium Slide Preparation: Sections for Xenium were prepared according to the Xenium In Situ for FFPE-Tissue Preparation Guide (CG000578 Rev C, 10X Genomics) protocol. Briefly, 5-μm sections were cut, floated in an RNAse-free water bath, and carefully placed onto the 10.45 mm x 22.45 mm sample area of Xenium slides (PN-3000941, 10X Genomics). The slides were then placed on a drying rack at room temperature for 30 minutes to remove excess water. This was followed by a 3-hour incubation at 42 ̊C on a Xenium Thermocycler Adapter plate, positioned atop the 96-well block of a C1000 Touch Thermal Cycler (BioRad) with the lid open. Subsequently, the slides were stored overnight at room temperature with a desiccant to facilitate further drying. The slides were then processed following the Xenium In Situ for FFPE Deparaffinization and Decrosslinking protocol (CG000580 Rev C, 10X Genomics). The slides were placed again on a Xenium Thermocycler Adapter plate atop the 96-well block of a thermocycler with the lid open and incubated at 60 ̊C for 2 hours. They were then equilibrated to room temperature for 7 minutes, deparaffinized, and rehydrated by immersion twice in xylene for 10 minutes each, twice in 100% ethanol for 3 minutes each, twice in 96% ethanol for 3 minutes each, once in 70% ethanol for 3 minutes, and once in water for 20 seconds. Subsequently, the Xenium slides were assembled into Xenium cassettes and hydrated with 1X PBS. The tissue sections were reverse crosslinked using a decrosslinking buffer containing tissue enhancer, urea, and perm enzyme B, at 80 ̊C for 30 minutes, followed by three washes with PBS-T. Slides were then immediately processed following the Xenium In Situ Gene Expression user guide (CG000582 Rev E, 10X Genomics) for the remaining slide preparation steps. Briefly, the pre-designed gene expression probe set, Xenium Human Multi-Tissue and Cancer Panel (10X-1000626, 10X Genomics) targeting 377 human genes, was utilized for prostate cancer, ileum, appendix, pancreas, and colon samples. For breast cancer samples, the Xenium Human Breast Panel (10X-1000463, 10X Genomics) targeting 380 human genes was used. Panels were denatured at 95 ̊C for 2 minutes, crash-cooled on ice for 1 minute, and then equilibrated to room temperature before being added to the probe hybridization buffer and TE buffer to make the probe hybridization mix. The slides were incubated with the hybridization mix at 50 ̊C for 17 hours. Slides were washed three times with PBS-T for 1 minute each then incubated with a post-hybridisation wash buffer for 30 minutes at 37 ̊C. Slides were washed three times with PBS-T for 1 minute each and incubated with ligation mix for 2 hours at 37 ̊C. Three 1-minute PBS-T washes were followed by a 2-hour incubation at 30 ̊C with an amplification mix. Slides were then washed three times with TE buffer then three washes with 1X PBS for 1 minute each followed by incubation with reducing agent B for 10 minutes, washed once in 70% ethanol for 1 minute, twice in 100% ethanol then treated with autofluorescence solution for 10 minutes in the dark. Slides were washed three times with 100% ethanol for 2 minutes each then dried for 5 minutes at 37 ̊C before rehydrating with 1X PBS then PBS-T for 2 minutes. Slides were stained with a nuclei staining buffer for 1 minute at room temperature followed by three washes with PBS-T for 1 minute each in the dark. The slides were then assembled into Xenium Cassettes and loaded into the Xenium Analyzer for imaging and decoding. These procedures were uniformly followed at St. Jude Children's Research Hospital, Weill Cornell Medical Center, 10x Genomics, and the UoA, ensuring consistency in theFOVs across all four locations. Breast cancer samples processed as part of the 10x Genomics’ Catalyst Program followed the methods previously described (19); these experiments were carried out at 10X Genomics headquarters (Pleasanton, CA, USA). Sections from the prostate cancer samples were also subjected to Xenium Multimodal segmentation through an early access program and processed at the 10X Genomics headquarters (Pleasanton, CA). In brief, the procedure for in situ gene expression with cell segmentation staining was conducted following the Demonstrated Protocol for Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578 Rev C, 10X Genomics), the Xenium In Situ Gene Expression User Guide (CG000582 Rev F, 10X Genomics), and the Xenium In Situ Gene Expression Cell Segmentation User Guide (CG000749 Rev A, 10X Genomics). The combined protocol utilized the Xenium Human Multi-Tissue and Cancer Panel for in situ gene expression and the Xenium Cell Segmentation Staining Reagents add-on (PN-1000661, 10X Genomics) for segmentation staining. This add-on kit contains a single cocktail of Xenium Multi-Tissue Stain Mix (PN-2000991, 10X Genomics), which contains a cocktail of antibodies labeling the membranes (anti-ATP1A1/CD45/E-cadherin), antibodies labeling the cell interior (anti-alphaSMA/Vimentin) and a universal interior label against Ribosomal RNA (18S rRNA). Stain was then enhanced by the addition of Xenium Staining Enhancer reagent, followed by treatment of the sections with Xenium Autofluorescence Mix (PN-2000753, 10X Genomics) to diminish unwanted autofluorescence and enhance the signal-to-noise ratio in the tissue sections. Subsequently, Xenium Nuclei Staining Buffer (PN-2000762, 10x Genomics) was used to help the identification of tissues or regions of interest during the instrument's overview scan.  Xenium RNA to CosMx Protein slide preparation: Following completion of the Xenium RNA run, slides were removed from the instrument and stored in the Xenium cassette with PBS-T at 4C. After storage for up to 3 days, slides were washed three times in PBS-T for 1 minute each as recommended in Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709 Rev A, 10X Genomics), removed from the Xenium cassette and placed into a wash jar of 1X PBS for 5 minutes as described in CosMx SMI Manual Slide Preparation for Protein Assays (MAN-10185-01-1, NanoString), incubation frames were attached to the Xenium slide and tissue sections were covered with Buffer W and incubated at room temperature for 1 hour in the dark. Afterwards, MAN-10185-01-1 and MAN-10161-03-2 were followed as previously described in CosMx Protein slide preparation and CosMx SMI setup and data acquisition.

scan_protocol: CosMx SMI Setup and Data Acquisition: The setup and scan acquisition for the CosMx SMI instrument were carried out as detailed in the CosMx SMI Instrument User Manual   (MAN-10161-02-1 or MAN-10161-03-2, Software Version 1.1, NanoString). A new acquisition process was initiated through the CosMx SMI Control Center web interface. Prior to insertion into the CosMx Flow Cell Assembly Tool, the slides were carefully dried in the areas surrounding the imaging region. The process involved lowering the tailgate, placing the slide, and then securing it by raising the tailgate. After removing the adhesive backing, a new flow cell coverslip was precisely aligned above the slide's imaging area. The Assembly Tool's lid was closed securely to affix the coverslip to the slide, thus creating a functional CosMx flow cell. Following the assembly, 2X SSC was gently introduced through one of the flow cell ports to hydrate the tissue section. Subsequent steps included entering the flow cell configuration data into the Control Center interface, which comprised the flow cell's barcode and the slide's ID number. The prostate sections underwent scanning with Configuration C for the pre-bleaching profile and Configuration A for the cell segmentation profile. Further details regarding the probe panel, cell segmentation, and supplemental markers were entered into the flow cell configuration data for each section. Assembled flow cells/slides, along with Buffer Bottles 1–4, were then loaded into the instrument. Before positioning Bottle 4, catalase and pyranose oxidase enzymes were added. The Control Center configuration was verified and following a period of equilibration to room temperature and the addition of an RNase inhibitor to a designated well in the CosMx imaging tray, the tray was placed in the instrument. A pre-run check and a tissue find scan for each tissue section were performed by the instrument. After the completion of tissue find scans, rectangular scan areas were delineated around each tissue section for the preview scan. The preview scan images facilitated the selection of a contiguous region of FOVs using the grid FOV placement tool, thoroughly covering the tissue areas on each slide. FOV selections for each slide were confirmed before initiating the cycling process. CosMx scan data were automatically uploaded to NanoString’s cloud-based AtoMx Spatial Analysis Platform during the run, as detailed in the CosMx Data Analysis manual (MAN-10162-02, Software Version 1.1, NanoString). Briefly, upon the completion of the run and the full upload of scan data to AtoMx, a study was created for each CosMx scan. Within AtoMx, pipelines were executed for each study, facilitating the export of data in various formats, such as TileDB arrays and Seurat objects, for in-house analysis.     Xenium Analyzer Setup and Data Acquisition: Xenium slides, assembled within Xenium cassettes, were imaged using the Xenium Analyzer, in accordance with the guidelines specified in the Xenium Analyzer User Guide (CG000584 Rev D and Rev E for Multi-modal Segmentation-stained slides, 10X Genomics). The Xenium Decoding Consumables Kit, (PN-1000487, 10X Genomics) was used for instrument loading. Briefly, Xenium slide ID numbers and information on pre-designed gene expression probes—were input into the Analyzer. The necessary consumables and reagents were loaded into the instrument: reagent module B, thawed at 4 ̊C overnight and equilibrated to room temp for 30 minutes prior to loading into the instrument, reagent module A, stored at 4 ̊C until loading in the instrument, instrument wash buffer (100% Milli-Q water), sample wash buffer A (1X PBS, 0.05% Tween-20), sample wash buffer B (100% Milli-Q water), and probe removal buffer (50% DMSO, 50 mM KCl, 0.1% Tween-20) were mixed prior to loading into the instrument with buffer caps along with, pipette tip rack, extraction tip, objective wetting consumable. After loading, the sample was scanned to generate images of the fluorescently labeled nuclei in each section which was used for FOV selection prior scanning. For the prostate cancer sample, the entire section was included in the full scan as 4 regions were selected for the appendix. After the run, the instrument was cleared of consumables, and the Xenium slides were carefully removed. Fresh PBS-T was applied to each slide/cassette, which were then   covered and stored in the dark at 4°C until post-run H&E staining. All procedures were standardized across three sites. The data were then acquired using the Xenium In Situ software suite (v1.9, 10X Genomics), which is a set of software applications for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer. For prostate samples stained with Multi-Modal Cell Segmentation reagents (10X Genomics Headquarters), both in situ gene expression and segmentation data were simultaneously collected and processed using v2.0 of the Xenium In Situ software suite.

data_processing:
To ensure a fair comparison, cells without detected transcripts were excluded from the analysis following the Xenium Onboard Analysis or the AtoMx processing workflow. Subsequent analyses, including cell type annotation, were conducted using raw transcript counts
Processed data: Transcript counts derived from intensity values within the boundaries of segmented cells.

source_name: PBMC, MCF-7

label_protocol: CosMx and Xenium barcoded probes for RNA and protein assays.

treatment_protocol: Normal and cencerous samples used for RNA and/or protein profiling (Xenium and CosMx platforms) as well as for tissue staining (Hematoxylin and Eosin, H&E) and single nuclei RNA-seq (snPATHO-Seq, using Chromium platform) were fixed in 10% neutral buffered formalin (NBF) and parafin embedeed (FFPE). To confirm the RNA quality of all the samples included in this study three consecutive 10-μm scrolls for the isolation and purification of total RNA (DV200 was used as measure of RNA intgrity post BioAnalyzer, TapeStation or Fragment Analyzer run). for snRNA-Seq from FFPE (snPATHO-Seq).

tag: tissue type

value: Blood and spiked-in MCF-7 cancer cells

tag: sample source

value: STEMCELL Technologies (PBMC), Swarbrick Lab (MCF-7, The Garvan Institute)

tag: sample processed

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

tag: sample type

value: Fixed cells

tag: replicate

tag: technology

tag: panel size


title: Siberian hamster, Amygdala, Long Photoperiod, Sample 4

description: Library name: Hamster Am 247


title: Medalist trial patient Responderj1376_samp2

description: Library name: j1376_samp2


title: Cflo_24_Mn4

city: Gainesville

first: Kayli

middle: Renee

last: Sieber

state: FL

address: 882 Newell Drive

department: Biology

institute: University of Florida

description: Library name: Cflo_24_Mn4

data_processing:
Mapping and alignment of reads to reference genomes were performed using Bowtie2 v2.2.9 and TopHat v2.1.1 in the cases of C. floridanus and A. cephalotes. For A. sexdens, de novo assembly was performed using Trinity v2.12.0.
Differential gene expression analysis was performed using DEseq2 v1.38.3
Assembly: Cflo_v7.5 and Attacep1.0
Supplementary files format and content: text files that contain raw counts for each sample

organism: Camponotus floridanus

source_name: antennae

extract_protocol:
Antennae were frozen with liquid nitrogen and ground into a fine dry powder using a pestle. RNA was extracted via a standard protocol using TRIzol Reagent, followed by ethanol precipitation. DNase treatment was performed in-solution, followed by a second round of TRIzol-chloroform and ethanol precipitation to remove the treatment.
We used the NEBNext Ultra II RNA Library Prep Kit for Illumina with an input of 100 ng RNA and 12 PCR cycles.

value: antennae

tag: batch


title: STAMP_07

source_name: MCF-7, SK-BR-3, LNCaP

value: Breast and prostate cancer cell lines mix

value: Butler and Swarbrick Lab (South Australian Health and Medical Research Institute, The Garvan Institute)


title: Medalist trial patient Responderj1376_samp3

description: Library name: j1376_samp3


title: Siberian hamster, Amygdala, Long Photoperiod, Sample 3

description: Library name: Hamster Am 248


title: Cflo_23_Mj4

description: Library name: Cflo_23_Mj4


title: STAMP_06


title: WJL4184_RLF_N034

description:
Library name: WJL4184
Jkappa1 coding end bait


title: STAMP_05

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)


title: Medalist trial patient Non-responderj1375_samp9

description: Library name: j1375_samp9

source_name: Medalist trial patient Non-responder


title: Siberian hamster, Amygdala, Long Photoperiod, Sample 2

description: Library name: Hamster Am 418


title: Medalist trial patient Responderj1376_samp1

description: Library name: j1376_samp1


title: STAMP_04

value: Single Molecule Imager

value: CosMx Human Universal Cell Characterization RNA Panel:1000


title: STAMP_10


title: Medalist trial patient Non-responderj1375_samp13

description: Library name: j1375_samp13

value: BMMNCs

value: Luspatercept


title: Cflo_21_Mj16

description: Library name: Cflo_21_Mj16


title: STAMP_03


title: Siberian hamster, Amygdala, Short Photoperiod, Sample 6

description: Library name: Hamster Am 288

value: Amygdala

value: Short 8L Photoperiod


title: Medalist trial patient Non-responderj1375_samp12

description: Library name: j1375_samp12


title: STAMP_08


title: Siberian hamster, Amygdala, Short Photoperiod, Sample 5

description: Library name: Hamster Am 278


title: Cflo_20_Mn15

description: Library name: Cflo_20_Mn15


title: STAMP_02

source_name: LNCaP

value: Prostate cancer cell line

value: Butler lab (South Australian Health and Medical Research Institute)


title: Cflo_22_Mn3

description: Library name: Cflo_22_Mn3


title: Medalist trial patient Non-responderj1375_samp11

description: Library name: j1375_samp11


title: Medalist trial patient Non-responderj1375_samp10

description: Library name: j1375_samp10


title: Cflo_18_Mn14

description: Library name: Cflo_18_Mn14


title: Cflo_19_Mj15

description: Library name: Cflo_19_Mj15


title: STAMP_01

source_name: PBMC

value: Blood

value: STEMCELL Technologies


title: Siberian hamster, Amygdala, Short Photoperiod, Sample 4

description: Library name: Hamster Am 289


title: WJL4187_RLF_N034

description:
Library name: WJL4187
Jkappa1 coding end bait

value: vAbl-ProB

value: pro-B cells


title: Siberian hamster, Amygdala, Short Photoperiod, Sample 3

description: Library name: Hamster Am 276


title: Cflo_17_Mj14

description: Library name: Cflo_17_Mj14

value: antennae


title: CD34+ d6 erythroid progenitors treated with GDF11j972_rna_d6G.TAGCTT.J972.AHJ5M5BGX7.L1-4.1

description: Library name: j972_rna_d6G.TAGCTT.J972.AHJ5M5BGX7.L1-4.1

value: In vitro HSC cultures


title: Siberian hamster, Amygdala, Long Photoperiod, Sample 1

description: Library name: Hamster Am 125

value: Long 16L Photoperiod


title: CD34+ d6 erythroid progenitors treated with vehiclej972_rna_d6C.ATCACG.J972.AHJ5M5BGX7.L1-4.1

description: Library name: j972_rna_d6C.ATCACG.J972.AHJ5M5BGX7.L1-4.1

value: Vehicle


title: Cflo_16_Mn13

description: Library name: Cflo_16_Mn13


title: SCSMV-2

city: Yangzhou

first: Zhen

last: He

state: Jiangsu province

address: Wenhui East Road No 4

department: Plant pathology

country: China

institute: Yangzhou University

description: Library name: Sample 5

data_processing:
The CleanReads are sequentially aligned with the designated reference genome using hisat2 to obtain the position information on the reference genome or gene, as well as the sequence characteristic information specific to the sequencing samples.
Assembly: Saccharum spontaneum AP85-441
Supplementary files format and content: tab-delimited text include RPKM values for each Sample

organism: Saccharum officinarum

source_name: leave

extract_protocol:
Total RNA was extracted using the Plant RNA Extraction Kit (column method) (T105096).
Poly (A) RNA from 1 mg total RNA or purified mRNA and purified m6A-containing fragments were used to generate the cDNA libraries, respectively, according to TruSeq RNA Sample Prep Kit protocol.

value: leave

value: SCSMV-infected


title: SCSMV-1

description: Library name: Sample 4


title: CK3

description: Library name: Sample 3

value: healthy


title: Cflo_15_Mj13

description: Library name: Cflo_15_Mj13


title: Siberian hamster, Amygdala, Short Photoperiod, Sample 1

description: Library name: Hamster Am 277


title: RNA_sgTAF6L_Replicate

city: Houston

first: Mo-Fan

last: Huang

state: TX

address: 6431 Fannin Street

department: Integrative Biology and Pharmacology

institute: University of Texas Health science center

data_processing:
Data processing step was completed by Novogene data analysis pipeline.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files include FPKM values for each sample
Supplementary files format and content: tab-delimited txt file includes DEGs list for TAF6L overexpression

source_name: Human Stomach

extract_protocol:
Total RNA were extracted using the RNeasy Mini Kit (Qiagen).
The mRNA library construction and sequencing were completed by Novogene.
The resulting libraries were sequenced 2 x 75 bp on an Illumina NextSeq500.

value: Human Stomach

value: TAF6L knockout


title: Siberian hamster, Hippocampus, Long Photoperiod, Sample 6

description: Library name: Hamster Hp 141

source_name: Hippocampus

value: Hippocampus


title: Cflo_14_Mn12

description: Library name: Cflo_14_Mn12


title: Siberian hamster, Hippocampus, Long Photoperiod, Sample 5

description: Library name: Hamster Hp 238


title: Siberian hamster, Amygdala, Short Photoperiod, Sample 2

description: Library name: Hamster Am 268

value: Amygdala

value: Short 8L Photoperiod


title: CK2

description: Library name: Sample 2


title: RNA_sgControl_Replicate

value: WT


title: Siberian hamster, Hippocampus, Long Photoperiod, Sample 4

description: Library name: Hamster Hp 247


title: CK1

description: Library name: Sample 1


title: SCSMV-3

description: Library name: Sample 6


title: Siberian hamster, Hippocampus, Long Photoperiod, Sample 3

description: Library name: Hamster Hp 248


title: Cflo_11_Mj11

description: Library name: Cflo_11_Mj11


title: hESC_Biological_2

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description:
Library name: hESC_Biological_2
other line summaries.txt
lane8789_CCAACA_TCTTTCCC_AW_Nucleo_R1_AW1_L001_UMIed_AGTC_index1_E8_Fisher_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated using a copy number aware UMI deduplicator. Pipeline available at https://github.com/laurabiggins/TrAEL-seq
Samples were imported into Seqmonk v1.48.2, truncated to a single base, then quantified either as total read count or as strand bias (R-F)/(R+F) equivalent to RFD.
Assembly: GRCh38
Supplementary files format and content: Annotated Probe Report for cut TAs and 1000 random.txt

extract_protocol:
½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl multiplexed TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: 1-2x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE.

value: Embryonic Stem Cells

value: Essential 8 Medium


title: Siberian hamster, Hippocampus, Long Photoperiod, Sample 2

description: Library name: Hamster Hp 418


title: RNA_TAF6L-GFP

value: TAF6L overexpression


title: Cflo_09_Mj7

description: Library name: Cflo_09_Mj7


title: RNA_Control


title: hESC_Biological_1

description:
Library name: hESC_Biological_1
other line summaries.txt
lane8789_CCAACA_TCTTTCCC_AW_Nucleo_R1_AW1_L001_UMIed_AAGG_index5_E8_SCT_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

value: TeSR-E8 media


title: Cflo_10_Mn7

description: Library name: Cflo_10_Mn7

value: antennae


title: Siberian hamster, Hippocampus, Long Photoperiod, Sample 1

description: Library name: Hamster Hp 125


title: Cflo_08_Mn1

description: Library name: Cflo_08_Mn1


title: DLD1_DRB

description:
Library name: DLD1_DRB
other line summaries.txt
lane8789_CATGGC_TCTTTCCC_AW_DRB_AW1_L001_UMIed_CTTG_index3_DRB_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

value: colorectal adenocarcinoma


title: ATAC_TAF6L-GFP_Replicate

data_processing:
Briefly, adapter sequences were removed using Cutadapt, and filtered reads were aligned to the hg38 reference genome using Bowtie2.
Picard was used to remove duplicated reads (https://broadinstitute.github.io/picard/), and reads with a quality score below 30 were filtered out. To verify data quality,
the insert size distribution was examined to confirm peaks around 50 bp and 200 bp. Peak calling was performed using MACS2, accounting for the specific 9 bp insertions introduced by the Tn5 transposase.
Finally, peaks were converted to BigWig format for visualization using IGV and downstream analyses.
Assembly: hg38
Supplementary files format and content: bigWig files are provided for each sample

extract_protocol:
ATAC-seq assay and libraries were prepared at the MD Anderson Epigenomics Profiling Core
ATAC-seq assay and libraries were prepared at the MD Anderson Epigenomics Profiling Core
The resulting libraries were sequenced 2 x 75 bp on an Illumina NextSeq500.


title: Siberian hamster, Hippocampus, Short Photoperiod, Sample 6

description: Library name: Hamster Hp 288


title: RNA_sgTAF6L


title: Siberian hamster, Hippocampus, Short Photoperiod, Sample 5

description: Library name: Hamster Hp 278


title: ATAC_TAF6L-GFP


title: Ug_T_40

city: Elon

first: Gregory

last: Haenel

state: NC

address: CB 2625, Elon University

institute: Elon University

data_processing:
After removing adapters and assessing read quality with the Trim Galore package (Version 0.6.4), the paired end reads from each individual were aligned to the Sceloporus undulatus annotated genome using the alignment tool STAR with the default settings.
Counts for expression analyses were made using featuresCounts in the Subread package
Gene expression was characterized using DESeq2
Assembly: GCF_019175285.1  NCBI Sceloporus undulatus Annotation Release 100
Supplementary files format and content: comma delimited file that contains counts for each sample outputted from DESeq2

organism: Urosaurus graciosus

source_name: Urosaurus graciosus (parental)

extract_protocol:
Liver tissue was homogenized in  TRIzol  using a Dounce glass homogenizer. After 5 min incubation at room temperature, chloroform was added. This was then shaken for 15 sec and incubated for 2-3min at room temperature. The homogenate was then centrifuged at 12,000g at 4oC for 15 minutes. RNeasy columns (Quigan) were then used following the manufacturers protocol
Illumina directional RNA library preparation was done by NC State Genomic Sciences Laboratory

value: liver

tag: Sex

value: male


title: Cflo_07_Mj1

description: Library name: Cflo_07_Mj1


title: DLD1_DMSO

description:
Library name: DLD1_untreated
other line summaries.txt
lane8789_CATGGC_TCTTTCCC_AW_DRB_AW1_L001_UMIed_AGTC_index1_Untreated_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: Siberian hamster, Hippocampus, Short Photoperiod, Sample 4

description: Library name: Hamster Hp 289


title: RNA_sgControl


title: ATAC_sgTAF6L


title: Ug_S_36


title: Siberian hamster, Hippocampus, Short Photoperiod, Sample 3

description: Library name: Hamster Hp 276


title: Ug_R_36


title: Cflo_05_Mj10

description: Library name: Cflo_05_Mj10


title: ATAC_sgControl_Replicate


title: Cflo_04_Mn9

description: Library name: Cflo_04_Mn9


title: Cflo_12_Mn11

description: Library name: Cflo_12_Mn11


title: Ug_Q_40


title: ATAC_sgControl


title: Siberian hamster, Hippocampus, Short Photoperiod, Sample 1

description: Library name: Hamster Hp 277


title: ATAC_Control_Replicate


title: Cflo_02_Mn8

description: Library name: Cflo_02_Mn8


title: Ug_P_40


title: ATAC_Control


title: ATAC_sgTAF6L_Replicate


title: Asex_3-Sol

description: Library name: Asex_3-Sol

organism: Atta sexdens


title: Hy_I_40

organism:
Urosaurus graciosus
Urosaurus ornatus

source_name: hybrid lizard


title: Cflo_01_Mj2

description: Library name: Cflo_01_Mj2


title: Hy_D_36


title: Uo_O_40

organism: Urosaurus ornatus

source_name: Urosaurus ornatus (parental)


title: Hy_X_40


title: Uo_N_40


title: Asex_3-For

description: Library name: Asex_3-For


title: Asex_2-Sol

description: Library name: Asex_2-Sol


title: Cflo_06_Mn10

description: Library name: Cflo_06_Mn10


title: Siberian hamster, Hippocampus, Short Photoperiod, Sample 2

description: Library name: Hamster Hp 268


title: Uo_L_40


title: Hy_B_36


title: Cflo_03_Mj9

description: Library name: Cflo_03_Mj9


title: Hy_A_36


title: Hy_K_40


title: Uo_H_36


title: Ug_J_36


title: E15.5 wild type 4

city: New York

first: Simone

last: Sanna-Cherchi

address: 1150 St.Nicholas Ave

department: Department of Medicine, Nephrology

institute: Columbia University

description:
Library name: MS016
Column name in WT_RankedByMeanFPKM.txt: MS016

data_processing:
30 million single-end 100bps reads were obtained per sample. RTA (Illumina) was used for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format and adaptor trimming.
Reads were mapped to the reference genome NCBI37/mm9 with Tophat version 2.1.0 with settings: 4 mismatches and 10 maximum multiple hits.
The relative abundance of genes and splice isoforms were estimated with cufflinks (version 2.0.2) with default settings to obtain FPKM values for each gene.
Assembly: mm9
Supplementary files format and content: tab-delimited text file including genes and FPKM values of each sample.

source_name: Kidney

extract_protocol:
Microdissected kidneys were submerged in RNAlater (Qiagen), then homogenized using micropestele (Avantor #211-2100). Total RNA was purified by RNeasy mini kit (Qiagen) according to manufacturer’s instructions.
Quantification and quality control were done by Bioanalyzer (now Agilent) followed by Illumina TruSeq library preparation and sequencing with Illumina Hiseq2500.

value: Kidney


title: E15.5 wild type 3

description:
Library name: MS015
Column name in WT_RankedByMeanFPKM.txt: MS015


title: E15.5 wild type 1

description:
Library name: MS013
Column name in WT_RankedByMeanFPKM.txt: MS013


title: E15.5 wild type 2

description:
Library name: MS014
Column name in WT_RankedByMeanFPKM.txt: MS014


title: DTX, scRNAseq

city: Bunkyo-ku

first: Hiroyuki

last: Koike

state: Tokyo

address: 1-5-45 Yushima

department: Department of Medical Biochemistry

country: Japan

institute: Institute of Science Tokyo

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded ptocessing, gene counting, and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Wound tissue of back skin

extract_protocol:
Mouse wound bed and back skin were captured by 10mm punch, minced with scissors, and digested with 125 µg/ml Liberase TL (Roche, Basel, Switzerland) in RPMI. Minced samples were incubated at 37C for 1 hour 20 minutes with rotation, filtered through 70-µm and 40-µm filters, spun down, and resuspended in 2% FBS / PBS. 7AAD (BD Pharmingen, CA, USA) was added immediately before sorting. Live cells (7AAD-negative) sorting was performed on BD FACSAria III with FACS DIVA software (BD Biosciences, CA, USA).
Single-cell capturing and library generation were performed using Chromium Single Cell 3’ Reagents Kits v3 (10x Genomics, CA, USA) as the manufacturer’s protocol. The sorted cells were resuspended at a concentration of approximately 1,000 cells/µL in PBS containing 0.04% BSA, and we targeted 10,000 cells per sample for capture. A single cell suspension was mixed with RT-PCR master mix and loaded with Single Cell 3’ v3 Gel Beads and Partitioning Oil onto Chromium Chip. The chip was then loaded onto a Chromium Controller for single-cell GEM generation. Immediately following GEM generation, the Gel Bead is dissolved, primers are released, and any co-partitioned cell is lysed. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA. After GEM disruption, full-length cDNA is amplified to generate sufficient mass library construction. Finally, amplified cDNAs were fragmented, and adapter and sample index were added into finished libraries.

value: Wound tissue of back skin

tag: strain

tag: age

value: 7-9 weeks old

value: Live cell

value: Diphtheria toxin (DTX)


title: Uo_F_36


title: Asex_1-For

description: Library name: Asex_1-For


title: Uo_E_36


title: cranial suture tissue, day 3, 1

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

description:
Library name: Sample1
cranial suture tissue, day 3

data_processing:
Thermo Fisher Torrent Suite V5.10 used for basecalling.
Thermo Fisher Torrent Suite V5.10 used for alignment.
Thermo Fisher ampliSeqRNA V5.10 in Torrent Suite V5.10 used for reads counting.
Assembly: mm10
Supplementary files format and content: csv
Supplementary files format and content: chp

source_name: cranial suture

extract_protocol:
Total RNA was isolated from the mouse cranial suture tissues, including coronal, sagittal, and lambdoid sutures of postnatal day 3 pups using RNA Mini Kit (Thermo Fisher, 12183018A) according to the manufacturer’s instruction.
The libraries were constructed using the Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit (Thermo Fisher, A36412) according to the manufacturer’s instructions.

value: cranial suture

value: Suture stem cells

value: wildtype


title: PBS, scRNAseq

value: PBS


title: cranial suture tissue, day 3, 2

description:
Library name: Sample2
cranial suture tissue, day 3


title: Ctrl_Deep-seq_RhCas12f1_Replicate2_additional_5sites

status: Public on Jun 22 2025

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

description: Library name: Ctrl_Deep-seq_RhCas12f1-add_Rep2

data_processing:
Raw paired-end reads were subjected to sublibrary barcode removal (first 6 bp) using cutadapt.
Reads were then aligned to their respective reference sequences using Bowtie 2.
Editing events were quantified using CRISPResso2.
Assembly: hg38
Supplementary files format and content: txt file for indel rate for gRNA taget sites.

source_name: MCF7 cell line

growth_protocol: MCF7 cells were maintained inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
Two round PCR were performed, the forward and reverse primers were used to amplify the target site of the first round of PCR, and then an equal amount of the first PCR product was mixed with primers containing P5 and p7 for a second round of PCR to generate the library.

treatment_protocol: In 24-well plates, MCF7 cells were transfected with 490ng gRNA plasmids and 10ng CasMINI or hpCasMINI or SpCas9 or LbCas12a plasmids.

value: MCF7 cell line

value: epithelial cell


title: exoRhCas12f1_Deep-seq_RhCas12f1_Replicate3_additional_5sites

description: Library name: exoRhCas12f1_Deep-seq_RhCas12f1-add_Rep3


title: exoRhCas12f1_Deep-seq_RhCas12f1_Replicate1_additional_5sites

description: Library name: exoRhCas12f1_Deep-seq_RhCas12f1-add_Rep1


title: Eppk1 knockout

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

description: Library name: HK02002

data_processing:
BCL files were demultiplexed using cellranger mkfastq (10x Genomics) with sample indexes SI-TS-G2 and barcodes BC003 (wildtype) and BC004 (knockout) to generate FASTQ files.
FASTQ files were processed using Cell Ranger (10x Genomics) with the Fixed RNA Profiling workflow (cellranger multi) using the mm10 transcriptome reference provided by 10x Genomics for probe mapping.
Assembly: mm10 (GRCm38) mouse reference genome, provided by 10x Genomics for Fixed RNA Profiling, was used for alignment and transcript quantification.
Supplementary files format and content: Processed data includes matrices in a .mtx.gz format, along with the associated barcodes.tsv and features.tsv files.

source_name: whole skin

growth_protocol: Murine skin samples were harvested from wild-type and Eppk1 knockout mice.

extract_protocol:
Whole murine skin samples were processed using the Miltenyi Biotec Skin Dissociation Kit, following the manufacturer's instructions to obtain viable single-cell suspensions. After enzymatic dissociation, cells were filtered to remove debris and aggregates. The resulting suspensions were then fixed and processed using the 10x Genomics Chromium Fixed RNA Profiling (Single Cell Flex) assay
Libraries were prepared using the 10x Genomics Chromium Fixed RNA Profiling (Flex) workflow with the Mouse Transcriptome Probe Kit (PN-1000496), following User Guide CG000527, version F. Dual indexing was performed using the SI-TS-G2 index. Library construction included PCR amplification (9 cycles), pooled wash workflow, and final QC via bioanalyzer.Wildtype sample barcode: BC003. Knockout sample barcode: BC004 Library QC metrics included average library size and concentration; both samples passed QC.

treatment_protocol: No experimental treatment was applied prior to tissue collection. Mice were sacrificed, and skin was directly processed for downstream single-cell RNA sequencing.

value: whole skin

value: Eppk1 knockout


title: wildtype

description: Library name: HK02001


title: Ctrl_Deep-seq_RhCas12f1_Replicate3_additional_5sites

description: Library name: Ctrl_Deep-seq_RhCas12f1-add_Rep3


title: Ctrl_Deep-seq_RhCas12f1_Replicate1_additional_5sites

description: Library name: Ctrl_Deep-seq_RhCas12f1-add_Rep1


title: Asex_2-For

description: Library name: Asex_2-For

value: antennae


title: exoRhCas12f1_Deep-seq_RhCas12f1_Replicate2_additional_5sites

description: Library name: exoRhCas12f1_Deep-seq_RhCas12f1-add_Rep2


title: enRhCas12f1_Deep-seq_RhCas12f1_Replicate3_additional_5sites

description: Library name: enRhCas12f1_Deep-seq_RhCas12f1-add_Rep3


title: enRhCas12f1_Deep-seq_RhCas12f1_Replicate2_additional_5sites

description: Library name: enRhCas12f1_Deep-seq_RhCas12f1-add_Rep2


title: Asex_1-Sol

description: Library name: Asex_1-Sol


title: enRhCas12f1_Deep-seq_RhCas12f1_Replicate1_additional_5sites

description: Library name: enRhCas12f1_Deep-seq_RhCas12f1-add_Rep1


title: Ctrl_Deep-seq_Replicate2_additional_7sites

description: Library name: Ctrl_Deep-seq_add_Rep2


title: Ctrl_Deep-seq_Replicate1_additional_7sites

description: Library name: Ctrl_Deep-seq_add_Rep1


title: exoCasMINI_Deep-seq_Replicate3_additional_7sites

description: Library name: exoCasMINI_Deep-seq_add_Rep3


title: Ctrl_Deep-seq_Replicate3_additional_7sites

description: Library name: Ctrl_Deep-seq_add_Rep3


title: exoCasMINI_Deep-seq_Replicate1_additional_7sites

description: Library name: exoCasMINI_Deep-seq_add_Rep1


title: exoCasMINI_Deep-seq_Replicate2_additional_7sites

description: Library name: exoCasMINI_Deep-seq_add_Rep2


title: CasMINI_Deep-seq_Replicate2_additional_7sites

description: Library name: CasMINI_Deep-seq_add_Rep2


title: Tag-seq of exoRhCas12f in the MCF7 cells (6sites)

description: Library name: Add-exoRhCas12f

data_processing:
The analysis pipeline can be accessed at https://github.com/zhoujj2013/Tag-seq
Assembly: hg38
Supplementary files format and content: Bed file for all cutting sites

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
The gDNA was fragmented, end-repaired, and ligated by dA-tail.


title: Tag-seq of exoCasMINI in the MCF7 cells (16sites)

description: Library name: MCF7-exoCasMINI


title: Tag-seq of enRhCas12f in the MCF7 cells (6sites)

description: Library name: Add-enRhCas12f


title: CasMINI_Deep-seq_Replicate3_additional_7sites

description: Library name: CasMINI_Deep-seq_add_Rep3


title: CasMINI_Deep-seq_Replicate1_additional_7sites

description: Library name: CasMINI_Deep-seq_add_Rep1


title: Tag-seq of CasMINI in the MCF7 cells (16sites)

description: Library name: MCF7-CasMINI


title: Tag-seq of CasMINI in the 293T cells

description: Library name: 293T-CasMINI

source_name: 293T cell line

value: 293T cell line

value: human embryonic kidney


title: SW480 Con-2

city: jinan

first: Guixi

last: Zheng

address: 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province

institute: Qilu Hospital of Shandong University

description:
Library name: 5
CT2

data_processing:
GLC Genomics Workbench v11.0.1
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 GrCM3B/mm 10 using CLC genomicbenchwork (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 genomics benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SW480 cells were cultured in Leibovitz’s L-15 medium supplemented with 10% FBS, under CO₂-free conditions at 37°C

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

value: colorectal adenocarcinoma

value: WT


title: Tag-seq of exoCasMINI in the 293T cells

description: Library name: 293T-exoCasMINI


title: SW480 DDX39B-3

description:
Library name: 3
OE3

value: DDX39B overexpression


title: SW480 DDX39B-1

description:
Library name: 1
OE1


title: SW480 Con-1

description:
Library name: 4
CT1


title: SW480 Con-3

description:
Library name: 6
CT3


title: Evaluation of the editing specificity of enRhCas12f1 in the MCF7 cells

data_processing:
The analysis pipeline can be accessed at https://github.com/zhoujj2013/Tag-seq
Assembly: hg38
Supplementary files format and content: Bed file for all cutting sites
Library strategy: Tag-Seq


title: Evaluation of the editing specificity of exoRhCas12f1 in the MCF7 cells


title: Evaluation of the editing specificity of exoCasMINI in the MCF7 cells, comparring with other CRISPR system


title: Evaluation of the editing specificity of LbCas12a in the MCF7 cells, comparring with other CRISPR system


title: Evaluation of the editing specificity of CasMINI in the MCF7 cells, comparring with other CRISPR system


title: Evaluation of the editing specificity of exoCasMINI in the MCF7 cells, comparing with CasMINI


title: exoCasMINI_L8_Deep-seq_gRNA-truncated_Replicate3

data_processing:
Raw paired-end reads were subjected to sublibrary barcode removal (first 6 bp) using cutadapt.
Reads were then aligned to their respective reference sequences using Bowtie 2.
Editing events were quantified using CRISPResso2.
Assembly: hg38
Supplementary files format and content: txt file for indel rate for gRNA taget sites.
Library strategy: Deep-Seq

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 3


title: exoCasMINI_L10_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 2


title: Evaluation of the editing specificity of CasMINI in the MCF7 cells, comparing with exoCasMINI


title: exoCasMINI_L8_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 2


title: exoCasMINI_L10_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 3


title: exoCasMINI_L8_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 1


title: exoCasMINI_L6_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 2


title: exoCasMINI_L4_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 3


title: exoCasMINI_L4_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 2


title: exoCasMINI_L6_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 3


title: exoCasMINI_L4_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 1


title: SW480 DDX39B-2

description:
Library name: 2
OE2


title: exoCasMINI_L2_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 1


title: exoCasMINI_L0_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, no truncated gRNA repeat 3


title: Evaluation of the editing specificity of enRhCas12f1 in the MCF7 cells for site SITE1


title: Evaluation of the editing specificity of exoRhCas12f1 in the MCF7 cells for site SITE1


title: Evaluation of the editing specificity of SpCas9 in the MCF7 cells, comparring with other CRISPR system


title: exoCasMINI_L2_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 3


title: exoCasMINI_L0_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, no truncated gRNA repeat 2


title: CasMINI_L10_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 2


title: exoCasMINI_L2_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 2


title: CasMINI_L10_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 1


title: CasMINI_L10_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 3


title: CasMINI_L8_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 3


title: CasMINI_L6_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 3


title: exoCasMINI_L10_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 10 base truncated gRNA repeat 1


title: CasMINI_L8_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 1


title: exoCasMINI_L6_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 1


title: CasMINI_L6_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 1


title: CasMINI_L4_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 3


title: CasMINI_L6_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 6 base truncated gRNA repeat 2


title: CasMINI_L4_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 2


title: CasMINI_L0_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, no truncated gRNA repeat 3


title: CasMINI_L4_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 4 base truncated gRNA repeat 1


title: CasMINI_L0_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, no truncated gRNA repeat 2


title: CasMINI_L0_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, no truncated gRNA repeat 1


title: CasMINI_L2_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 1


title: CasMINI_L2_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 2


title: Ctrl_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or exoCasMINI system targeting two different genomic sites, repeat 3


title: exoCasMINI_DM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

description: Indel_rates_of_gRNA_mismatch-NLRC4.txt.gz

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 10 repeat 2


title: exoCasMINI_DM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 9 repeat 3


title: exoCasMINI_DM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 10 repeat 3


title: exoCasMINI_DM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 9 repeat 2


title: exoCasMINI_DM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 10 repeat 1


title: exoCasMINI_L0_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting two different genomic sites, no truncated gRNA repeat 1


title: Ctrl_Deep-seq_gRNA-truncated_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or exoCasMINI system targeting two different genomic sites, repeat 1


title: Ctrl_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or exoCasMINI system targeting two different genomic sites, repeat 2


title: exoCasMINI_DM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 9 repeat 1


title: exoCasMINI_DM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 7 repeat 3


title: exoCasMINI_DM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 8 repeat 2


title: CasMINI_L8_Deep-seq_gRNA-truncated_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 8 base truncated gRNA repeat 2


title: exoCasMINI_DM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 6 repeat 3


title: exoCasMINI_DM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 7 repeat 2


title: exoCasMINI_DM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 8 repeat 3


title: exoCasMINI_DM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 7 repeat 1


title: CasMINI_L2_Deep-seq_gRNA-truncated_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, 2 base truncated gRNA repeat 3


title: exoCasMINI_DM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 6 repeat 1


title: exoCasMINI_DM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 5 repeat 3


title: exoCasMINI_DM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 6 repeat 2


title: exoCasMINI_DM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 5 repeat 2


title: exoCasMINI_DM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 5 repeat 1


title: exoCasMINI_DM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 4 repeat 2


title: exoCasMINI_DM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 4 repeat 1


title: exoCasMINI_DM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 3 repeat 2


title: exoCasMINI_DM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 3 repeat 1


title: exoCasMINI_DM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 3 repeat 3


title: exoCasMINI_DM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 2 repeat 3


title: exoCasMINI_DM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 2 repeat 2


title: exoCasMINI_DM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 1 repeat 3


title: exoCasMINI_DM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 8 repeat 1


title: exoCasMINI_SM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 10 repeat 3


title: exoCasMINI_SM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 10 repeat 2


title: exoCasMINI_DM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 1 repeat 1


title: exoCasMINI_DM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 2 repeat 1


title: exoCasMINI_DM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 1 repeat 2


title: exoCasMINI_SM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 10 repeat 1


title: exoCasMINI_SM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 9 repeat 3


title: exoCasMINI_SM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 9 repeat 2


title: exoCasMINI_SM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 8 repeat 1


title: exoCasMINI_SM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 7 repeat 2


title: exoCasMINI_SM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 8 repeat 2


title: exoCasMINI_SM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 7 repeat 1


title: exoCasMINI_SM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 6 repeat 3


title: exoCasMINI_SM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 6 repeat 2


title: exoCasMINI_SM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 5 repeat 3


title: exoCasMINI_DM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, double mismatch gRNA site 4 repeat 3


title: exoCasMINI_SM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 5 repeat 1


title: exoCasMINI_SM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 8 repeat 3


title: exoCasMINI_SM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 5 repeat 2


title: exoCasMINI_SM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 4 repeat 2


title: exoCasMINI_SM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 4 repeat 3


title: exoCasMINI_SM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 7 repeat 3


title: exoCasMINI_SM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 4 repeat 1


title: exoCasMINI_SM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 3 repeat 2


title: exoCasMINI_SM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 3 repeat 3


title: exoCasMINI_SM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 6 repeat 1


title: exoCasMINI_SM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 9 repeat 1


title: exoCasMINI_SM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 3 repeat 1


title: exoCasMINI_SM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 2 repeat 1


title: exoCasMINI_SM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 1 repeat 3


title: exoCasMINI_SM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 1 repeat 2


title: exoCasMINI_SM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 2 repeat 3


title: exoCasMINI_SM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 2 repeat 2


title: exoCasMINI_Full_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, complete gRNA repeat 2


title: exoCasMINI_Full_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, complete gRNA repeat 1


title: exoCasMINI_Ctrl_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the exoCasMINI system targeting NLRC4, repeat 3


title: exoCasMINI_Full_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, complete gRNA repeat 3


title: exoCasMINI_Ctrl_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the exoCasMINI system targeting NLRC4, repeat 2


title: CasMINI_DM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 10 repeat 3


title: CasMINI_DM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 10 repeat 2


title: CasMINI_DM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 9 repeat 2


title: CasMINI_DM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 10 repeat 1


title: exoCasMINI_Ctrl_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the exoCasMINI system targeting NLRC4, repeat 1


title: CasMINI_DM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 9 repeat 3


title: CasMINI_DM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 9 repeat 1


title: CasMINI_DM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 8 repeat 3


title: CasMINI_DM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 8 repeat 1


title: CasMINI_DM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 8 repeat 2


title: CasMINI_DM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 7 repeat 1


title: CasMINI_DM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 7 repeat 3


title: CasMINI_DM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 6 repeat 2


title: CasMINI_DM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 6 repeat 3


title: exoCasMINI_SM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting NLRC4, single mismatch gRNA site 1 repeat 1


title: CasMINI_DM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 5 repeat 2


title: CasMINI_DM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 4 repeat 2


title: CasMINI_DM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 4 repeat 1


title: CasMINI_DM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 5 repeat 3


title: CasMINI_DM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 4 repeat 3


title: CasMINI_DM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 3 repeat 2


title: CasMINI_DM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 5 repeat 1


title: CasMINI_DM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 2 repeat 3


title: CasMINI_DM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 3 repeat 3


title: CasMINI_DM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 2 repeat 1


title: CasMINI_DM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 1 repeat 3


title: CasMINI_DM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 1 repeat 2


title: CasMINI_DM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 1 repeat 1


title: CasMINI_SM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 10 repeat 3


title: CasMINI_DM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 2 repeat 2


title: CasMINI_SM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 10 repeat 2


title: CasMINI_SM10_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 10 repeat 1


title: CasMINI_SM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 9 repeat 1


title: CasMINI_SM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 9 repeat 3


title: CasMINI_SM9_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 9 repeat 2


title: CasMINI_DM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 7 repeat 2


title: CasMINI_SM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 8 repeat 3


title: CasMINI_SM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 8 repeat 2


title: CasMINI_DM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 6 repeat 1


title: CasMINI_SM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 7 repeat 3


title: CasMINI_SM8_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 8 repeat 1


title: CasMINI_SM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 7 repeat 2


title: CasMINI_SM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 6 repeat 3


title: CasMINI_SM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 6 repeat 1


title: CasMINI_SM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 5 repeat 1


title: CasMINI_SM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 4 repeat 3


title: CasMINI_SM6_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 6 repeat 2


title: CasMINI_SM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 4 repeat 1