title: RNA-seq_Cbfb-MYH11-mDE_rep1

description: Library name: RNA-seq_Cbfb-MYH11-mDE_rep1


title: D(froR) 4 uM H2O2 rep1 (AS9)

status: Public on Jun 23 2025

type: SRA

city: Irvine

first: Albert

last: Siryaporn

state: CA

address: 4129 Reines Hall

country: USA

institute: University of California Irvine

description: Library name: Sample9

library_source: transcriptomic

data_processing:
Adapters were trimmed in Trimmomatic version 0.39
Reads were aligned using aligner Bowtie2 version 2.5.4
Processed count table was generated using FeatureCounts in Subread version 2.0.8
Assembly: NC_008463.1
Supplementary files format and content: raw counts and normalized counts of transcript on CDS (coding sequence) and sRNA (non coding region)

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: bacterial culture

growth_protocol: 18 hours in a roller drum spinning at 200 rpm at 37 °C MinA minimal medium, which contains per 1 L of water: 4.5 g KH2PO4, 10.5 g K2HPO4, 1 g (NH4)2SO4, 1 mM MgSO4 and 0.2 % (w/v) sodium citrate

extract_protocol:
RNA was harvested using Macherey-Nagel NucleoSpin RNA purification kit.
Library construction was performed by UCI Genomics High-Throughput Facility (GHTF) using Nextera DNA library prep kit.

treatment_protocol: 1:1000 dilution of the overnight culture, 2.5 hour outgrowth, and stimulated with NaOCl, H2O2, or untreated for 0.5 hour.

tag: cell type

value: bacterial culture

tag: genotype

value: D(froR)

tag: treatment


title: WT1M

city: Barcelona

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

country: Spain

institute: Sequientia Biotech

data_processing:
RNA-seq read quality control (QC) analyses and filtering of high-quality reads were executed using FastQC and BBDuk (Bushnell et al. 2017) by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were aligned to the mouse genome reference (GrCm38p6/mm10) with STAR 2.7.3a (Dobin et al. 2012), while FeatureCounts 1.6.3 package (Liao et al. 2014) was used to assign reads to genes.
Genes with low, constant levels of raw counts across one or more experimental conditions were filtered out using HTSFilter 1.30.1 (Rau et al. 2013). Filtered gene data was further processed with the EdgeR package (Robinson et al. 2009) to normalize the raw counts.
Assembly: GRCz11
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with fpkm normalized gene counts for every gene and every sample

organism: Danio rerio

source_name: Intestine

extract_protocol:
Trizol
TruSeq Stranded mRNA LT Sample Prep Kit was used. The Poly-A containing mRNA molecules are purified using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was done using DNA Polymerase I and RNase H, followed by 5' and 3' adapter ligation. Adapter-ligated fragments were then PCR amplified and gel purified.

tag: tissue

value: Intestine

value: Tubingen


title: STAMP_73

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.

organism: Homo sapiens

source_name: Tongue cancer CAFs

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

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.

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: Cancer-associated fibroblasts (CAFs) isolated from tongue squamous cell carcinoma

tag: sample source

value: Dr. Marina Kochetkova (University of South Australia)

tag: sample processed

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

tag: sample type

value: Fixed cells

tag: replicate

value: r1, r2:Replicate slide 2/2

tag: technology

value: Single Molecule Imager

tag: panel size

value: CosMx Human 6K Discovery Panel:6000


title: STAMP_72

value: Human glioblastoma-astrocytoma cell line


title: RNA-seq_control_rep3

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: Library name: RNA-seq_control_rep3

data_processing:
For ChIC-seq: Paired-end raw reads were mapped to mouse genome mm10 by Bowtie2 (v2.3.5)57 and converted into bigwig files with reads per million (RPM) signals for aggregation analysis and visualization in WashU Genome Browser.  For RNA-seq: Raw reads were mapped to mouse genome mm10 with STAR (v2.5.1b)53. The gene expression levels were quantified and normalized by cuffnorm from cufflinks (v2.2.1)54 package into an FPKM matrix. Genes were filtered off if their expression levels < 1 FPKM in all samples. The expression matrix was further log2-transformed. The differentially expressed genes (DEGs) were called with cuffdiff (v2.2.1),55 requiring q-value <0.01, absolute fold change between the two conditions >=2, the sum of mean expression level between the two conditions >=1 and genes in the filtered expression matrix. The enriched GO terms were identified by findGO.pl from HOMER package (v4.10.4)56, requiring at least 5 genes in the target biological process term, fewer than 500 total genes in the term,  and a p-value < 1e-5. Ingenuity Pathway Analysis (Ingenuity Systems) was performed to identify upstream regulators of the DEGs; For scRNA-seq: Reads were pre-processed with cellranger count (v7.2.0) (10x Genomics). Cells were retained for subsequent analysis if they expressed at least 500 genes, had fewer than 5% of reads mapping to mitochondrial genes, and had more than 5% of reads mapping to ribosomal genes. These cells were then normalized and integrated with our previous study data using Seurat (v4.2.1). All cells UMAP visualization and marker genes for the four populations were also obtained with Seurat. Cells classified as the AMP populations were extracted, and their normalized expression matrix was used to obtain the first two component values for each cell with the PCA implemented in scikit-learn package (https://scikit-learn.org/stable/). The first two components were then fed to UMAP (https://umap-learn.readthedocs.io/en/latest/) with key parameters: n=100, init='pca', metric='euclidean', min_dist=0.0, n_epochs=1000, andom_state =123. The AMP UMAP results were clustered using HDBSCAN (v0.8.33) (https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html) with key parameters: min_samples=1000,min_cluster_size=100. Differentially expressed genes within the AMP cells between clusters were identified using a two-sided Wilcoxon rank-sum test implemented in the Scipy package (v1.11.3)61 (scipy.stats.ranksums), with criteria of p-value < 1e-10, absolute fold change >=2, and expression in more than 20% of cells in at least one condition.
Assembly: mm10
Supplementary files format and content: ChIP-seq: BigWig files containing normalized reads per million (RPM) signals. RNA-seq: Text files containing gene expression matrices quantified using RPKM (Reads Per Kilobase of transcript per Million reads). 10x scRNA-seq: H5 files generated by the Cell Ranger pipeline.

molecule: polyA RNA

organism: Mus musculus

source_name: Mice LSK cells

extract_protocol:
Total RNA were extracted with AllPrep DNA/RNA/Protein Mini Kit (QIAGEN)
ChIC-seq libraries were constructed as previously described (Ku, W.L., et al., Nature Methods, 16, 323-325). RNA-seq libraries were prepared using poly(A) enrichment and  the Illumina TruSeq Stranded mRNA Sample Prep Kits according to manufacturer’s instructions. 10x scRNA-seq libraries were generated following the manufacturer’s instructions.

treatment_protocol: For ChIC-seq, wildtype (WT), Mx1-CreCbfb+/56M(dHABD), Mx1-CreCbfb+/56M-ΔHABD (dHABD) and Mx1-CreCbfb+/56M-mDE (mDE) mice were injected with pIpC and 2-3 weeks later, the LK population in the bone marrow cells of these mice were sorted out. For RNA-seq, (1) wildtype (WT), Mx1-CreCbfb+/56M(dHABD), Mx1-CreCbfb+/56M-ΔHABD (dHABD) and Mx1-CreCbfb+/56M-mDE (mDE) mice were injected with pIpC and 2-3 weeks later, the LK population in the bone marrow cells of these mice were sorted out; (2) Mx1-CreCbfb+/56M (Mx1CreKI) and Runx1+/R188QMx1-CreCbfb+/56M (R188QCreKI) mice were injected with pIpC and 83 weeks later, the LK population in the bone marrow cells of these mice were sorted out.

value: Mice LSK cells

value: wild type

value: pIpC


title: D(froR) 1 uM NaOCl rep1 (AS8)

description: Library name: Sample8

value: NaOCl


title: STAMP_71

value: Human erythroleukemia cell line

value: Dr. Winnie Kan (University of South Australia)


title: ASIP9M


title: WT5H


title: RNA-seq_control_rep1

description: Library name: RNA-seq_control_rep1


title: AL143 uninduced rep2 (AS7)

description: Library name: Sample7

value: bacterial culture

value: WT


title: STAMP_69

value: Immortalized human pancreatic beta cell line

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


title: ASIP16H

value: Intestine


title: ChIC-seq_KI_Runx1_rep1

description:
Library name: ChIC-seq_KI_Runx1_rep1
anti RUNX1

library_source: genomic

data_processing:
For ChIC-seq: Paired-end raw reads were mapped to mouse genome mm10 by Bowtie2 (v2.3.5)57 and converted into bigwig files with reads per million (RPM) signals for aggregation analysis and visualization in WashU Genome Browser.  For RNA-seq: Raw reads were mapped to mouse genome mm10 with STAR (v2.5.1b)53. The gene expression levels were quantified and normalized by cuffnorm from cufflinks (v2.2.1)54 package into an FPKM matrix. Genes were filtered off if their expression levels < 1 FPKM in all samples. The expression matrix was further log2-transformed. The differentially expressed genes (DEGs) were called with cuffdiff (v2.2.1),55 requiring q-value <0.01, absolute fold change between the two conditions >=2, the sum of mean expression level between the two conditions >=1 and genes in the filtered expression matrix. The enriched GO terms were identified by findGO.pl from HOMER package (v4.10.4)56, requiring at least 5 genes in the target biological process term, fewer than 500 total genes in the term,  and a p-value < 1e-5. Ingenuity Pathway Analysis (Ingenuity Systems) was performed to identify upstream regulators of the DEGs; For scRNA-seq: Reads were pre-processed with cellranger count (v7.2.0) (10x Genomics). Cells were retained for subsequent analysis if they expressed at least 500 genes, had fewer than 5% of reads mapping to mitochondrial genes, and had more than 5% of reads mapping to ribosomal genes. These cells were then normalized and integrated with our previous study data using Seurat (v4.2.1). All cells UMAP visualization and marker genes for the four populations were also obtained with Seurat. Cells classified as the AMP populations were extracted, and their normalized expression matrix was used to obtain the first two component values for each cell with the PCA implemented in scikit-learn package (https://scikit-learn.org/stable/). The first two components were then fed to UMAP (https://umap-learn.readthedocs.io/en/latest/) with key parameters: n=100, init='pca', metric='euclidean', min_dist=0.0, n_epochs=1000, andom_state =123. The AMP UMAP results were clustered using HDBSCAN (v0.8.33) (https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html) with key parameters: min_samples=1000,min_cluster_size=100. Differentially expressed genes within the AMP cells between clusters were identified using a two-sided Wilcoxon rank-sum test implemented in the Scipy package (v1.11.3)61 (scipy.stats.ranksums), with criteria of p-value < 1e-10, absolute fold change >=2, and expression in more than 20% of cells in at least one condition.
Assembly: mm10
Supplementary files format and content: ChIP-seq: BigWig files containing normalized reads per million (RPM) signals. RNA-seq: Text files containing gene expression matrices quantified using RPKM (Reads Per Kilobase of transcript per Million reads). 10x scRNA-seq: H5 files generated by the Cell Ranger pipeline.
Library strategy: CUT&Run

molecule: genomic DNA


title: AL143 4 uM H2O2 rep3 (AS5)

description: Library name: Sample5


title: ASIP13H


title: STAMP_68

source_name: hESC

value: human Embryonic Stem Cells

value: Sullivan Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)

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


title: AL143 4 uM H2O2 rep2 (AS4)

description: Library name: Sample4


title: ASIP14H


title: ASIP11M


title: ASIP10M


title: STAMP_66

source_name: LNCaP

value: Prostate cancer cell line

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

value: Fixed cells

value: r1, r2:Replicate slide 2/2

value: Single Molecule Imager


title: AL143 4 uM H2O2 rep1 (AS3)

description: Library name: Sample3


title: ChIC-seq_KI_IgG_rep1

description:
Library name: ChIC-seq_KI_IgG_rep1
anti IgG

value: Mice LSK cells

value: pIpC


title: ChIC-seq_KI_H3K27ac_rep1

description:
Library name: ChIC-seq_KI_H3K27ac_rep1
anti H3K27ac


title: AL143 1 uM NaOCl rep1 (AS1)

description: Library name: Sample1

value: NaOCl


title: STAMP_65

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)

value: CosMx Human 6K Discovery Panel:6000


title: RNA-seq_control_rep2

description: Library name: RNA-seq_control_rep2

value: wild type


title: AL143 uninduced rep1 (AS6)

description: Library name: Sample6

value: bacterial culture

value: WT


title: STAMP_70

value: Immortalized human mammary epithelial cell line

value: Sweeney Lab (South Australian immunoGENomics Cancer Institute, The University of Adelaide)


title: STAMP_64

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


title: U2OS cells, disome fraction, crosslinked, rep2

city: Heidelberg

first: Günter

last: Kramer

address: Im Neuenheimer Feld 329

country: Germany

institute: Center for Molecular Biology of Heidelberg University (ZMBH)

description:
Library name: U2OS_Dis_CL_rep2
Footprints (approx. 30nt) from Disome fraction

data_processing:
The 3' adaptor sequences were trimmed form demultiplexed raw read sequencing files with Cutadapt (v1.13) with the following command for NextSeq550 files: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz. For samples sequenced on HiSeq2000 the following command was used: cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz
Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (available as supplement information in Bertolini et al., 2021) with the following command: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 2. Only samples 5-8 did not contain UMI sequences in the adaptors, therefore this step was not included for U2OS samples.
For removal of human rRNA contaminants, sequenced libraries were aligned to rRNA sequences including: RNA45SN1 - RNA45SN5 (human 28S, 18S, 5.8S), RNA5S1 (human 5S), MTRNR2L10 (Mito 16S), MT-RNR1 (Mito 12S), MT-RNR2U1 (Mito 16S), 22 mito tRNAs, 631 nuclear human tRNAs. All rRNA contaminations were removed by Bowtie2 (v.2.3.5.1) with the following command: bowtie2 -p4 -t -x <path_to_folder_with_Bowtie-indexed_rRNA_contamination> -q <path_to_input_file>.fastq.gz' --un <path_to_output_file>.fastq -S /dev/null
Reads that did not align to rRNA were aligned to the human genome (GRCh38p10) using STAR (v2.7.1a) with the following command: STAR --runThreadN 24 --genomeDir <path_to_indexed_genome> --readFilesIn <path_to_input>.fastq --outFilterMultimapNmax 1 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix <path_to_output> --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
All reads aligning to the coding sequence (CDS) were assigned (a-, p-, e-site) via a custom Julia script (available as supplement information in Bertolini et al., 2021). p-site assigned reads were used for all downstream analysis. This script accounts for soft-clipping via the '-c 1' option: the integer indicates the bases at the 5' end that often arise from untemplated addition by the reverse transcriptase during library preparation by using the following command: julia <path_to_script>/Script2.jl -c 1 -g <path_to_genome_annotation>.gff' -u -o <path_to_output> <path_to_input>.bam
Assembly: Human genome (GRCh38p10)
Supplementary files format and content: HDF5 files containing raw reads assigned to ribosomal P-sites, organised by coding sequence (CDS). Depending on the library preparation method PCR duplicates are removed based on the unique molecular identifier (UMI).
Library strategy: Ribo-Seq

source_name: Osteosarcoma

growth_protocol: Human cells were cultivated in DMEM with GlutaMAX, pyruvate, 10% FCS, pen/strep, 37°C, 5% CO2, humidified. Cells were passaged regularly through trypsinization. For all experiments cells were seeded 18-24 hours before lysis in 15 cm2 dishes (3.5 million U2OS and 6 million HEK293-T cells) to reach 70-90% confluency at the time of harvesting.

extract_protocol:
RNA from frozen ribosome fractions was extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019
Libraries from isolated ribosome footprints were prepared following the previously published protocol (Galmozzi and Merker et al. 2019)

value: Osteosarcoma

tag: cell line

tag: fraction

value: disome fraction

value: 2.5 mM BS3 and 20 mM EDC in 150 mM KCl-containing lysis buffer


title: ChIC-seq_dHABD_MYH11_rep1

description:
Library name: ChIC-seq_dHABD_MYH11_rep1
anti MYH11


title: SOX2,NSC197,rep1

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

description: Library name: SOX2_NSC197_rep1

data_processing:
The quality of the fastq files was accessed using FastQC  (Ref. 1) and MultiQC (Ref. 2).
Illumina adapters and low-quality reads were filtered out using BBDuk (v.38.87)
Bowtie2 (v.2.3.4.3) (Ref. 4) was used to align the sequencing reads to the hg38 reference human genome.
Samtools (v.1.11) (Ref. 4) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool
The normalization ratio for each sample was calculated by dividing the number of uniquely mapped human reads of the sample with the lowest number of reads by the number of uniquely mapped human reads of each sample.
These normalization ratios were used to randomly sub-sample reads to obtain the same number of reads for each sample using using samtools view -s.
Bigwig files were created using deepTools bamCoverage (Ref. 7) and visualized using IGV (Ref. 8).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

growth_protocol: GBMs were then cultured in Neurocult Complete (NCC) media, a defined and commercially available serum-free neural stem cell medium (STEMCELL Technologies, Cat#05751), supplemented with human recombinant epidermal growth factor (20ng/mL: STEMCELL Technologies, Cat#78006), basic fibroblast growth factor (20ng/mL; STEMCELL Technologies Cat#78006), heparin (2 μg/mL 0.2% Heparin Sodium Salt in PBS; STEMCELL technologies, Cat#07980), antibiotic-antimycotic (1X; Wisent, Cat# 450-115-EL). Tumorspheres derived from these cultures were expanded on polyornithine-laminin coated plates for adherent growth until sufficient populations were acquired for experimental purposes. Passaging consisted of dissociating a 10cm dish with 1 mL of TrypLE (ThermoFisher Cat. 25200056) for 5 min at 37°C followed by collection with PBS and centrifugation at 300g. Neural stem cells were derived and propagated in a similar fashion, as previously published (Suk 2022, STAR Protocols).

extract_protocol:
Patient-derived lines were acquired and propagated as previously described. CUT&RUN was performed using a magnetic bead-based protocol using the CUTANA Kit (EpiCypher Cat.14-1048) according to the manufacturer’s instructions. The magnet was placed on ice for all steps. Cells were harvested by centrifugation (300g for 3 minutes at room temperature in a swinging bucket rotor) and washed in ice cold Wash Buffer. One million cells were added to low-binding PCR tubes containing activated beads (in triplicate) for 10 minutes at room temperature. Cell Permeabilization Buffer consisted of Wash Buffer containing 0.01% Digitonin. Antibody Buffer consisted of Cell Permeabilization Buffer containing 0.5M EDTA). 0.5ug of each antibody (SOX2-test, H3K4me4-positive control, and IgG-negative control) was added to respective tubes and placed on a nutator overnight at 4ºC for incubation. Extracted DNA fragments were quantified using a QubitTM fluorometer and stored at -20ºC until library preparation was initiated.
Library preps were conducted using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions. Sequencing libraries were prepared by amplifying DNA fragments using a 2-step PCR using primers as follows: R1: 5'-[insert]-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC...-3' and R2: 5'-[insert]-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT...-3'. The resulting libraries were subsequently sequenced on an Illumina HiSeq2500 (RRID: SCR_016383).

value: Brain normal cell


title: SOX2,MBT103,rep2

description: Library name: SOX2_MBT103_rep2

value: Brain cancer cell


title: U2OS cells, disome fraction, crosslinked, rep1

description:
Library name: U2OS_Dis_CL_rep1
Footprints (approx. 30nt) from Disome fraction


title: ChIC-seq_KI_MYH11_rep1

description:
Library name: ChIC-seq_KI_MYH11_rep1
anti MYH11

value: Mice LSK cells


title: STAMP_62

source_name: BM CD34+

value: Bone marrow-derived hematopoietic stem cells

value: STEMCELL Technologies

value: Fixed cells

value: Single Molecule Imager


title: U2OS cells, monosome fraction, crosslinked, rep2

description:
Library name: U2OS_Mono_CL_rep2
Footprints (approx. 30nt) from monosome fraction

value: monosome fraction


title: STAMP_63

source_name: PBMC

value: Blood

value: r1, r2:Replicate slide 2/2

value: CosMx Human 6K Discovery Panel:6000


title: SOX2,MBT103,rep1

description: Library name: SOX2_MBT103_rep1


title: SOX2,BT954,rep2

description: Library name: SOX2_BT954_rep2


title: U2OS cells, monosome fraction, crosslinked, rep1

description:
Library name: U2OS_Mono_CL_rep1
Footprints (approx. 30nt) from monosome fraction

value: wild type


title: STAMP_67

source_name: iPSC 32F

value: induced Pluripotent Stem Cells

value: Polo Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)


title: ChIC-seq_mDE_Runx1_rep1

description:
Library name: ChIC-seq_mDE_Runx1_rep1
anti RUNX1

value: pIpC


title: STAMP_60

source_name: MD3 iTSC

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

value: r1, r2:Replicate slide 1/2


title: ChIC-seq_dHABD_H3K27ac_rep1

description:
Library name: ChIC-seq_dHABD_H3K27ac_rep1
anti H3K27ac


title: AL143 1 uM NaOCl rep2 (AS2)

description: Library name: Sample2

value: bacterial culture

value: WT

value: NaOCl


title: SOX2,NSC197,rep2

description: Library name: SOX2_NSC197_rep2

value: Brain normal cell


title: ChIC-seq_mDE_MYH11_rep1

description:
Library name: ChIC-seq_mDE_MYH11_rep1
anti MYH11

value: Mice LSK cells


title: GBM8-DMSO-24h-1

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

description: Library name: GBM8-DMSO-24h-1

data_processing:
Fastqs aligned and quantified using STAR
Assembly: hg38
Supplementary files format and content: raw_counts_GBM8_CT179.csv [raw counts matrix from STAR quantmode]

growth_protocol: GBM8 cells (Primary, IDHwt, Female, Classical, EGFR amp, MGMT methylated) were obtained from the Mayo Clinic Brain Tumor Patient-Derived Xenograft National Resource.

extract_protocol:
GBM8 cells were treated with 100nM CT-179, 200 nM CT-179, or vehicle control, and RNA was extracted following a 24 hour treatment period
TruSeq

value: DMSO


title: SOX2,BT935,rep2

description: Library name: SOX2_BT935_rep2

value: Brain cancer cell


title: STAMP_58

source_name: KELLY

value: Human neuroblastoma cell line

value: Goodall Lab (University of South Australia)

value: Fixed cells

value: Single Molecule Imager


title: ChIC-seq_mDE_IgG_rep1

description:
Library name: ChIC-seq_mDE_IgG_rep1
anti IgG


title: GBM8-DMSO-24h-2

description: Library name: GBM8-DMSO-24h-2


title: GBM8-DMSO-24h-3

description: Library name: GBM8-DMSO-24h-3


title: SOX2,BT935,rep1

description: Library name: SOX2_BT935_rep1


title: ChIC-seq_dHABD_Runx1_rep1

description:
Library name: ChIC-seq_dHABD_Runx1_rep1
anti RUNX1


title: STAMP_59

source_name: MD3 iPSC

value: CosMx Human 6K Discovery Panel:6000


title: ChIC-seq_mDE_H3K27ac_rep1

description:
Library name: ChIC-seq_mDE_H3K27ac_rep1
anti H3K27ac


title: IgG,NSC197,rep2

description: Library name: IgG_NSC197_rep2


title: STAMP_61

source_name: MD3 HDF

value: induced Pluripotent Stem Cells


title: ChIC-seq_WT_Runx1_rep1

description:
Library name: ChIC-seq_WT_Runx1_rep1
anti RUNX1

value: wild type


title: STAMP_56

source_name: SK-N-SH


title: IgG,MBT103,rep2

description: Library name: IgG_MBT103_rep2


title: IgG,NSC197,rep1

description: Library name: IgG_NSC197_rep1


title: STAMP_55

source_name: SK-N-DZ


title: GBM8-CT179-100nM-24h-1

description: Library name: GBM8-CT179-100nM-24h-1


title: ChIC-seq_dHABD_IgG_rep1

description:
Library name: ChIC-seq_dHABD_IgG_rep1
anti IgG

value: pIpC


title: GBM8-CT179-100nM-24h-3

description: Library name: GBM8-CT179-100nM-24h-3


title: ChIC-seq_WT_MYH11_rep1

description:
Library name: ChIC-seq_WT_MYH11_rep1
anti MYH11


title: GBM8-CT179-100nM-24h-2

description: Library name: GBM8-CT179-100nM-24h-2


title: GBM8-CT179-200nM-24h-1

description: Library name: GBM8-CT179-200nM-24h-1


title: ChIC-seq_WT_IgG_rep1

description:
Library name: ChIC-seq_WT_IgG_rep1
anti IgG


title: IgG,MBT103,rep1

description: Library name: IgG_MBT103_rep1


title: IgG,BT954,rep2

description: Library name: IgG_BT954_rep2


title: STAMP_54

value: Derivative of the human embryonic kidney 293 (HEK293) cell line, modified to express the SV40 large T antigen

value: Dr. Jason Gummow (Functional Genomics South Australia and Gene Silencing and Expression Laboratory, The University of Adelaide)

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


title: STAMP_53

value: r1, r2:Replicate slide 1/2


title: SOX2,BT954,rep1

description: Library name: SOX2_BT954_rep1


title: ChIC-seq_WT_H3K27ac_rep1

description:
Library name: ChIC-seq_WT_H3K27ac_rep1
anti H3K27ac


title: STAMP_52

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

value: Breast and prostate cancer cell lines mix

value: Butler, Swarbrick Lab, Goodall Labs (South Australian Health and Medical Research Institute, The Garvan Institute, University of South Australia)


title: IgG,BT954,rep1

description: Library name: IgG_BT954_rep1


title: Myc-Cap, YJ1206 treated 24 hr - 2

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description: Library name: SI_38751

data_processing:
FASTQs were trimmed using BBDuk. Transcripts were quantified by kallisto with mouse reference genome (GRCm38/mm10) and then summarized to obtain gene level counts and TPM.
Assembly: GRCm38
Supplementary files format and content: counts.csv: gene level counts for the six samples.
Supplementary files format and content: tpm.tsv: gene level TPM values for the six samples.

source_name: Myc-Cap

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and quantified by NanoDrop 2000 Spectrophotometers (Thermo Scientific).
RNA-seq libraries were prepared using KAPA RNA Hyper+RiboErase HMR (Roche Cat#: 08098140702). Ribosomal RNA was removed by enzymatic digestion from 800 ng total RNA, following with cDNA and double strand cDNA synthesis, end repair, A-tailing, and ligation with NEB adapters. cDNA fragments with sizes between 250-300 bp were separated using double AMPure beads and PCR amplified using 2x KAPA HiFi HotStart mix and NEB dual indexes (Roche Cat#: E6440L). Library quality was measured on an Agilent 2100 Bioanalyzer for concentration and product size. Paired-end libraries were sequenced with the Illumina NovaSeq 6000 (2 × 150 nucleotide read length) with sequence coverage to 20-30 million paired reads.

value: Myc-Cap


title: Myc-Cap, YJ1206 treated 24 hr - 3

description: Library name: SI_38752


title: Myc-Cap, YJ1206 treated 24 hr - 1

description: Library name: SI_38750


title: IgG,BT935,rep2

description: Library name: IgG_BT935_rep2


title: STAMP_51

value: Castration-resistant prostate cancer cell line derived from LNCaP cells


title: STAMP_57


title: IgG,BT935,rep1

description: Library name: IgG_BT935_rep1

value: Brain cancer cell


title: DLD1_SSB_seq

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
Library name: DLD1_SSB_seq
other line summaries.txt
lane8669_CAAAAG_DLD-1_SSB-seq_Jon_WGS_GRCh38_rRNA_L001_GRCh38_rRNA_bowtie2

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: colorectal adenocarcinoma


title: STAMP_50

source_name: Oral cancer cell line (UM-SCC-1)

value: Human squamous cell carcinoma cell line

value: Dr. Marina Kochetkova (University of South Australia)


title: Myc-Cap, DMSO treated - 3

description: Library name: SI_37889

value: DMSO


title: STAMP_49

source_name: Tongue cancer CAFs

value: Cancer-associated fibroblasts (CAFs) isolated from tongue squamous cell carcinoma

value: Fixed cells

value: Single Molecule Imager

value: CosMx Human 6K Discovery Panel:6000


title: Myc-Cap, DMSO treated - 2

description: Library name: SI_37888


title: DLD1_Biological_2

description:
Library name: DLD1_Biological_2
other line summaries.txt
lane8112_CGTACG_TrAEL_index_pool_x7_B_L001_UMIed_TTCC_index6_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: H3K4me3,NSC197,rep1

description: Library name: H3K4me3_NSC197_rep1

value: Brain normal cell


title: H3K4me3,NSC197,rep2

description: Library name: H3K4me3_NSC197_rep2


title: GBM8-CT179-200nM-24h-3

description: Library name: GBM8-CT179-200nM-24h-3


title: NCI_H23_rep2

description:
Library name: NCI_H23_rep2
other line summaries.txt
lane7739_ATGTCA_NCI-H23_DMSO_L001_UMIed_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

value: lung adenocarcinoma


title: Myc-Cap, DMSO treated - 1

description: Library name: SI_37887


title: GBM8-CT179-200nM-24h-2

description: Library name: GBM8-CT179-200nM-24h-2


title: NCI_H23_rep1

description:
Library name: NCI_H23_rep1
other line summaries.txt
lane7739_AGTTCC_NCI-H23_control_L001_UMIed_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: NK_WTvTCF19_Timecourse_scRNAseq

city: New York

first: Celeste

last: Dang

state: NY

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis. After mitochondrial and doublet cleanup, raw count matrix was normalized by median library size normalization followed by log transformation.
The Louvain algorithm with k = 20 was used to perform clustering and Euclidean distance was used as the metric to construct nearest neighbor graph. MAST was then used to perform differential expression (DE) analysis between hash-ed samples, and GSEA enrichment analysis (https://github.com/zqfang/GSEApy) was then performed on DE genes (FDR < 0.05 & |coef| > 0) using ‘MSigDB_Hallmark_2020’ gene set and significant pathways were identified based on padj <0.05. In some cases, MAGIC was used to impute transcript counts.
Assembly: mm10
Supplementary files format and content: tag-list csv contains HTO sample information

source_name: Spleen

extract_protocol:
Spleens were dissociated and filtered through 100-μm cell strainer. Flow cytometry and cell sorting were performed on the Cytek Aurora (Cytek Biosciences) and Aria II cytometers (BD Biosciences), respectively. Before cell sorting, NK cells were enriched by incubating whole splenocytes with the following antibodies at 20 μg/ml against CD3ε (17A2), CD4 (GK1.5), CD8 (2.43), Ter119 (TER-119), CD19 (1D3), Ly6G (1A8) (BioXCell) followed by magnetic depletion using goat anti-rat beads (QIAGEN). For scRNA-seq enriched splenocytes were then stained with surface markers to identify Ly49H+ NK cells (CD3/TCRb/CD19- NK1.1+ CD49b+ Ly49H+) and sorted based on congenic markers (CD45.1 and CD45.2) to identify WT and Tcf19−/− cells with > 95% purity.
Ly49H+ NK cells (CD3/TCRb/CD19− NK1.1+ CD49b+ Ly49H+) from either WT or Tcf19-/- NK cells were sorted from spleens of MCMV-infected WT:Tcf19-/- adoptive transfer mice as described from day 0, 2, 4 and 7 PI, and stained with barcoded antibodies (Total-Seq B, Biolegend). After hash-staining, WT and Tcf19-/- Ly49H+ NK cells were mixed at 1:1 ratio for each time point. The single-cell RNA-seq from these pooled FACS-sorted cell suspensions was then performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) trypan blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Samples were multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO) following a previously published protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package.

value: Spleen

value: NK cell

value: MCMV infection

tag: library type

value: Hash Tag Oligonucleotides - HTO


title: H3K4me3,BT954,rep2

description: Library name: H3K4me3_BT954_rep2


title: H3K4me3,MBT103,rep1

description: Library name: H3K4me3_MBT103_rep1


title: DLD1_Technical_index8

description:
Library name: DLD1_Technical_index8
other line summaries.txt
lane8315_CCAACA_NK_Indexes_2_L001_UMIed_GCCA_index8_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: H3K4me3,MBT103,rep2

description: Library name: H3K4me3_MBT103_rep2


title: Sox2 RNAseq KO repeat 4

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Sox2 RNAseq KO repeat 4

data_processing:
Raw FASTQ reads were trimmed by Trimmomatic
Reads were aligned to mouse refenrence genome mm10 by STAR aligner
Assembly: mm10
Supplementary files format and content: TAB

source_name: Retina

extract_protocol:
Fresh retinae were placed in TRIReagent (Zymo Research R2050-1-50), and RNA was extracted according to Direct-zol RNA MiniPrep kit protocol (Zymo Research R2050).
The Illumina Stranded Total RNA Library Prep kit (Illumina, 20040529) was used following the manufacturer’s protocol for library preparation.

value: Retina

tag: age

value: Sox2 KO


title: STAMP_45

value: Immortalized human pancreatic beta cell line

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

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

value: r1, r2:Replicate slide 1/2


title: H3K4me3,BT954,rep1

description: Library name: H3K4me3_BT954_rep1

value: Brain cancer cell


title: CD-2217_TCF19_2_HTO

description: 10X Genomics

value: GEX


title: STAMP_46

value: Immortalized human mammary epithelial cell line

value: Sweeney Lab (South Australian immunoGENomics Cancer Institute, The University of Adelaide)

value: Fixed cells


title: DLD1_Technical_index7

description:
Library name: DLD1_Technical_index7
other line summaries.txt
lane8315_CCAACA_NK_Indexes_2_L001_UMIed_GTGC_index7_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

value: colorectal adenocarcinoma


title: DLD1_Merged_HiRes

description:
Library name: DLD1_Merged_HiRes_T
other line summaries.txt
dld-1_merged_sorted


title: STAMP_48

value: Human glioblastoma-astrocytoma cell line

value: Dr. Marina Kochetkova (University of South Australia)

value: Single Molecule Imager

value: CosMx Human 6K Discovery Panel:6000


title: H3K4me3,BT935,rep2

description: Library name: H3K4me3_BT935_rep2


title: Sox2 RNAseq KO repeat 3

description: Sox2 RNAseq KO repeat 3


title: DLD1_Biological_1

description:
Library name: DLD1_Biological_1
other line summaries.txt
lane8000_TAGCTT_DLD1_plug_pool_A_L001_UMIed_AGTC_index1_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: H3K4me3,BT935,rep1

description: Library name: H3K4me3_BT935_rep1


title: Sox2 RNAseq KO repeat 1

description: Sox2 RNAseq KO repeat 1


title: STAMP_43

value: induced Pluripotent Stem Cells

value: Polo Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)


title: STAMP_42

source_name: LNCaP

value: Prostate cancer cell line

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


title: STAMP_47

value: Human erythroleukemia cell line

value: Dr. Winnie Kan (University of South Australia)


title: Sox2 RNAseq KO repeat 2

description: Sox2 RNAseq KO repeat 2

value: Retina

value: Sox2 KO


title: DLD1_Technical_index5

description:
Library name: DLD1_Technical_index5
other line summaries.txt
lane8315_CCAACA_NK_Indexes_2_L001_UMIed_AAGG_index5_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: DLD1_Technical_index6

description:
Library name: DLD1_Technical_index6
other line summaries.txt
lane8315_CCAACA_NK_Indexes_2_L001_UMIed_TTCC_index6_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: DLD1_Technical_index3

description:
Library name: DLD1_Technical_index3
other line summaries.txt
lane8315_CCAACA_NK_Indexes_2_L001_UMIed_CTTG_index3_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: STAMP_41

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)

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

value: r1, r2:Replicate slide 1/2


title: WT RNAseq repeat 3

description: WT RNAseq repeat 3

value: WT


title: STAMP_44

source_name: hESC

value: human Embryonic Stem Cells

value: Sullivan Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)

value: Fixed cells


title: STAMP_40

value: Single Molecule Imager

value: CosMx Human 6K Discovery Panel:6000


title: DLD1_Technical_index1

description:
Library name: DLD1_Technical_index1
other line summaries.txt
lane8315_CCAACA_NK_Indexes_2_L001_UMIed_AGTC_index1_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

value: colorectal adenocarcinoma


title: WT RNAseq repeat 2

description: WT RNAseq repeat 2


title: STAMP_39

value: Blood

value: STEMCELL Technologies


title: K562 cells, SAR1A knockout CRISPR/Cas9 + HU, rep 2

first: Griffin

middle: P

last: Rodgers

state: MD

address: 10 Center Drive

department: NHLBI

institute: NIH

description: Library name: 120922_K562_SN2+HU

library_source: other

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low quality sequence and trim bases using Partek Flow
Trimemed sequence reads were mapped to Homo sapiens (human) hg38/miRBase mature microRNAs version 22
Read count extraction and normalization were performed using Partek Flow
Assembly: Homo sapiens (human) hg38/miRBase mature microRNAs version 22
Supplementary files format and content: tab-delimited text file includes raw microRNA counts for each sample

molecule: other

growth_protocol: K562 cells were cultured in RPMI medium containing 10% fetal bovine serum and 1× penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
miRNA was isolated by using an miRNeasy micro kit
miRNA samples were sequenced at Arraystar

treatment_protocol: Cells were treated with 100 uM hydroxyurea for 72 h.

value: human erythroleukemia cell line

value: SAR1A knockout

value: HU treatment


title: WT RNAseq repeat 1

description: WT RNAseq repeat 1

value: Retina


title: K562 cells, SAR1A knockout CRISPR/Cas9 + HU, rep 3

description: Library name: 061422_K562_SN3+HU


title: IMR90_HRASG12V_Day6_4

description:
Library name: IMR90_HRASG12V_Day6_4
IMR90 RFD and read counts.txt
lane8407_GAGTGG_Senescence_2_L001_UMIed_GTGC_index7_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1

source_name: IMR90 HRASG12V

value: IMR90 HRASG12V

value: Fibroblasts with inducible HRASG12V

value: DMEM


title: STAMP_38

source_name: PBMC treated with LPS  for 4h

value: LPS treated PBMC

value: Heyn Lab (Centro Nacional de Análisis Genómico)

value: r1, r2:Replicate 2

value: CosMx Human Universal Cell Characterization RNA Panel:1000


title: K562 cells, SAR1A knockout CRISPR/Cas9, rep 3

description: Library name: 061422_K562_SN3

value: no treatment


title: STAMP_37

value: Fixed cells

value: r1, r2:Replicate 1

value: Single Molecule Imager


title: K562 cells, SAR1A knockout CRISPR/Cas9, rep 2

description: Library name: 120922_K562_SN2


title: IMR90_HRASG12V_Day1_4

description:
Library name: IMR90_HRASG12V_Day1_4
IMR90 RFD and read counts.txt
lane8407_GAGTGG_Senescence_2_L001_UMIed_CTTG_index3_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: K562 cells, SAR1A knockout CRISPR/Cas9, rep 1

description: Library name: 052021_K562_SN1


title: STAMP_36

source_name: PBMC treated with LPS  for 24h


title: IMR90_HRASG12V_Day3_4

description:
Library name: IMR90_HRASG12V_Day3_4
IMR90 RFD and read counts.txt
lane8407_GAGTGG_Senescence_2_L001_UMIed_TTCC_index6_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: IMR90_HRASG12V_Day0_4

description:
Library name: IMR90_HRASG12V_Day0_4
IMR90 RFD and read counts.txt
lane8407_GAGTGG_Senescence_2_L001_UMIed_AGTC_index1_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: K562 cells, Wild type + HU, rep 3

description: Library name: 061422_K562_M3+HU

value: WT


title: IMR90_HRASG12V_Day3_3

description:
Library name: IMR90_HRASG12V_Day3_3
IMR90 RFD and read counts.txt
lane8407_CACGAT_Senescence_1_L001_UMIed_CTTG_index3_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: K562 cells, Wild type + HU, rep 2

description: Library name: 120922_K562_M2+HU


title: IMR90_HRASG12V_Day6_3

description:
Library name: IMR90_HRASG12V_Day6_3
IMR90 RFD and read counts.txt
lane8407_CACGAT_Senescence_1_L001_UMIed_TTCC_index6_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: K562 cells, Wild type + HU, rep 1

description: Library name: 052021_K562_M1+HU


title: STAMP_34

source_name: PBMC treated with vehicle  for 4h

value: Control PBMC


title: STAMP_35

source_name: PBMC treated withLPS  for 24h


title: K562 cells, SAR1A knockout CRISPR/Cas9 + HU, rep 1

description: Library name: 052021_K562_SN1+HU

value: human erythroleukemia cell line


title: STAMP_33


title: Sox2 KO ATACseq repeat 1

description: Sox2 KO ATACseq repeat 1

data_processing:
Raw FASTQ reads were trimmed by Trimmomatic
Reads were aligned to mouse refenrence genome mm10 by BWA
BAM filtering was performed by samtools and markduplicate by Picard tool
Peaks were called by MACS
BW was generated by bamCoverage
Assembly: mm10
Supplementary files format and content: BW

extract_protocol:
Dissociated E14.5 retinal cells were subjected to tagmentation reaction at 37°C for 30 min. DNA purification was carried out with a Qiagen MinElute PCR Purification Kit (Qiagen, 28006) and PCR amplification was performed using indexed primers.
The resulting library was quantified and assessed through a Qubit FLEX fluorometer and an Agilent TapeStation 4150 respectively. ATAC was performed using Active Motif ATAC-seq kit (Catalog No. 53150) according to the manufacturer’s protocol.

value: Sox2 KO


title: K562 cells, Wild type, rep 3

description: Library name: 061422_K562_M3


title: IMR90_HRASG12V_Day1_3

description:
Library name: IMR90_HRASG12V_Day1_3
IMR90 RFD and read counts.txt
lane8407_CACGAT_Senescence_1_L001_UMIed_AGTC_index1_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: K562 cells, Wild type, rep 2

description: Library name: 120922_K562_M2


title: IMR90_HRASG12V_Day0_3

description:
Library name: IMR90_HRASG12V_Day0_3
IMR90 RFD and read counts.txt
lane8407_CACGAT_Senescence_1_L001_UMIed_AAGG_index5_R1_trimmed_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: WT ATACseq repeat 2

description: WT ATACseq repeat 2


title: IMR90_HRASG12V_Day6_2

description:
Library name: IMR90_HRASG12V_Day6_2
IMR90 RFD and read counts.txt
lane8178_CCAACA_Senescence_pool_2_L001_UMIed_GCCA_index8_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: STAMP_31

source_name: PBMC treated with vehicle  for 24h


title: WT ATACseq repeat 1

description: WT ATACseq repeat 1


title: STAMP_30

source_name: PBMC treated with aCD3+aCD28 for 4h

value: aCD3+aCD28 treated PBMC


title: IMR90_HRASG12V_Day3_2

description:
Library name: IMR90_HRASG12V_Day3_2
IMR90 RFD and read counts.txt
lane8178_CCAACA_Senescence_pool_2_L001_UMIed_GTGC_index7_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: K562 cells, Wild type, rep 1

description: Library name: 052021_K562_M1


title: IMR90_HRASG12V_Day1_2

description:
Library name: IMR90_HRASG12V_Day1_2
IMR90 RFD and read counts.txt
lane8178_CCAACA_Senescence_pool_2_L001_UMIed_TTCC_index6_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: STAMP_29


title: Acep_Sol_5

city: Gainesville

first: Kayli

middle: Renee

last: Sieber

state: FL

address: 882 Newell Drive

department: Biology

institute: University of Florida

description: Library name: Acep_Sol_5

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: Atta cephalotes

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: NK cells, Wildtype, MCMV infection day 4, non enriched input, biol rep 1

first: Hyunu

last: Kim

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie2 (v2.4.1).
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as control using narrow peak parameters --cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
Peaks called by MACS2 for WT TCF19 d4 sample group and KO TCF19 d4 sample were filtered using q-values calculated via MACS2 to keep top 75% of the peaks. Then, these peaks were aggregated and merged via union to the peak atlas. This atlas were then further filtered to include only the peaks where two or all replicates within WT d4 TCF19 have top75% peaks called. The atlas was then annotated with UCSC mm10 Known Gene model.
Assembly: mm10
Supplementary files format and content: bigwig files are pileups of reads aligned to the reference genome and scaled using Saccharomyces cerevisiae spike-in DNA.
Supplementary files format and content: tsv file is tab delimited table of peak atlas
Library strategy: CUT&RUN

source_name: NK

extract_protocol:
400,000 sorted cells (50,000 for input) were washed thrice with PBS, resuspended in Buffer 1 (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in H2O) and incubated with TCF19 (anti-TCF19, Abcam ab230005) antibodies at 1/100 dilution in Antibody Buffer (Buffer 1 + 2uM EDTA) in 96 well V-bottom plate at 4C overnight. Upon antibody incubation, cells were washed twice with Buffer 1 and resuspended in 50ul of Buffer 1 + 1X pA/G-MNase (Cell Signaling #57813) and incubated on ice for 1 hr and washed with Buffer 2 (0.05% w/v Saponin, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS) three times. After washing, Calcium Buffer (Buffer 2 + 2uM of CaCl2) was used to resuspend the cells for 30 mins on ice to activate the pA/G-MNase reaction, and equal volume of 2X STOP Buffer (Buffer 2 + 20uM EDTA + 4uM EGTA) was added along with 1pg of Saccharomyces cerevisiae spike-in DNA (Cell Signaling #29987). Samples were incubated for 15 mins at 37C and DNA was isolated and purified using Qiagen MinElute Kit according to manufacturer’s protocol.
Immunoprecipitated DNA was quantified by PicoGreen, and the size was evaluated using an Agilent BioAnalyzer: fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter, A63882. KAPA HTP Library Preparation Kit (Kapa Biosystems, KK8234) was used to prepare Illumina sequencing libraries according to the manufacturer’s instructions with 0.4-1.4 ng input DNA and 14 cycles of PCR. Barcoded libraries were run on the NovaSeq 6000 in a PE100 run using S4 kit version 1.5 with XP mode to generate approximately 23 million paired reads per sample.

value: NK

tag: cell number

tag: celltype

tag: antibody

value: input

value: MCMV d4


title: NK cells, Wildtype, MCMV infection day 4, TCF19 antibody enriched, biol rep 3

tag: cell type

tag: genotype

tag: treatment


title: IMR90_HRASG12V_Day0_2

description:
Library name: IMR90_HRASG12V_Day0_2
IMR90 RFD and read counts.txt
lane8178_CCAACA_Senescence_pool_2_L001_UMIed_CTTG_index3_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

value: IMR90 HRASG12V

value: Fibroblasts with inducible HRASG12V

value: DMEM


title: Sox2 KO ATACseq repeat 2

description: Sox2 KO ATACseq repeat 2

tag: tissue

value: Retina


title: STAMP_28

source_name: PBMC treated with aCD3+aCD28 for 24h

tag: tissue type

tag: sample source

value: Heyn Lab (Centro Nacional de Análisis Genómico)

tag: sample processed

value: r1, r2:Replicate 2

value: CosMx Human Universal Cell Characterization RNA Panel:1000


title: Acep_Sol_4

description: Library name: Acep_Sol_4


title: STAMP_27

tag: sample type

value: Fixed cells

tag: replicate

value: r1, r2:Replicate 1

tag: technology

value: Single Molecule Imager


title: NK cells, Wildtype, MCMV infection day 4, TCF19 antibody enriched, biol rep 2

value: WT


title: NK cells, Wildtype, MCMV infection day 4, TCF19 antibody enriched, biol rep 1


title: Acep_Sol_3

description: Library name: Acep_Sol_3


title: STAMP_32

source_name: PBMC treated with vehicle for 24h

value: Control PBMC

tag: panel size


title: IMR90_HRASG12V_Day6_1

description:
Library name: IMR90_HRASG12V_Day6_1
IMR90 RFD and read counts.txt
lane8178_CATTTT_Senescence_pool_1_L001_UMIed_GTGC_index7_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

tag: cell line


title: STAMP_26

source_name: Differentiated iPSC 32F to Mesoderm

value: Differentiated iPSC 32F

value: Sullivan Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)

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


title: IMR90_HRASG12V_Day3_1

description:
Library name: IMR90_HRASG12V_Day3_1
IMR90 RFD and read counts.txt
lane8178_CATTTT_Senescence_pool_1_L001_UMIed_TTCC_index6_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: Acep_Sol_2

description: Library name: Acep_Sol_2

value: antennae


title: Acep_Sol_1

description: Library name: Acep_Sol_1


title: Acep_Mi_5

description: Library name: Acep_Mi_5


title: IMR90_HRASG12V_Day1_1

description:
Library name: IMR90_HRASG12V_Day1_1
IMR90 RFD and read counts.txt
lane8178_CATTTT_Senescence_pool_1_L001_UMIed_CTTG_index3_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1


title: STAMP_24

source_name: hESC H1 treated with BMP4  for 96h

value: BMP4 treated hEST H1


title: NK cells, Wildtype, naive, TCF19 antibody enriched, biol rep 1

value: NK

value: naive


title: NK cells, TCF19 knockout, MCMV infection day 4, TCF19 antibody enriched, biol rep 2

value: MCMV d4


title: NK cells, TCF19 knockout, MCMV infection day 4, non enriched input, biol rep 1

value: input


title: STAMP_23

source_name: hESC H1 treated with BMP4 for 72h


title: Acep_Mi_4

description: Library name: Acep_Mi_4


title: Acep_Mi_3

description: Library name: Acep_Mi_3


title: WJL4202_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: WJL4202
Jkappa1 coding end bait

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)

source_name: bone marrow

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.

value: bone marrow

value: pro-B cells

value: SetX-/-


title: STAMP_22

source_name: hESC H1 treated with BMP4 for 6h

value: Fixed cells

value: CosMx Human Universal Cell Characterization RNA Panel:1000


title: GDF11-Input

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

description: Library name: GDF11-Input

data_processing:
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2 with local read alignment
Peaks were called using MACS v2.1.0
Assembly: hg38
Supplementary files format and content: tab separated txt

source_name: HSC

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:
ChIP was performed using Diagenode Diagenode HighCell ChIP Kit (Cat# C01010060).
Illumina library prep kit was used to prepare ChIP-seq libraries

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

value: HSC

value: stem cells and progenitors


title: GDF11-Chip

description: Library name: GDF11-Chip


title: WJL4201_RLF_N034

description:
Library name: WJL4201
Jkappa1 coding end bait


title: Acep_Mi_2

description: Library name: Acep_Mi_2


title: STAMP_21

source_name: hESC H1 treated with BMP4 for 48

value: Single Molecule Imager


title: Acep_Mi_1

description: Library name: Acep_Mi_1


title: Control-Input

description: Library name: Control-Input


title: WJL4200_RLF_N034

description:
Library name: WJL4200
Jkappa1 coding end bait


title: STAMP_20

source_name: hESC H1 treated with BMP4 for 24h


title: Control-Chip

description: Library name: Control-Chip


title: Medalist trial patient Responderj1383_samp37

description: Library name: j1383_samp37

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

source_name: Medalist trial patient Responder

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

value: BMMNCs

value: Luspatercept


title: WJL4196_RLF_N034

description:
Library name: WJL4196
Jkappa1 coding end bait

value: SetX+/+


title: Acep_For_5

description: Library name: Acep_For_5

value: antennae


title: IMR90_HRASG12V_Day0_1

description:
Library name: IMR90_HRASG12V_Day0_1
IMR90 RFD and read counts.txt
lane8178_CATTTT_Senescence_pool_1_L001_UMIed_AGTC_index1_T_GRCh38_rRNA_bowtie2_dedup_umibam2.1

source_name: IMR90 HRASG12V

value: IMR90 HRASG12V

value: Fibroblasts with inducible HRASG12V

value: DMEM


title: WJL4197_RLF_N034

description:
Library name: WJL4197
Jkappa1 coding end bait


title: STAMP_25

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: iPSC 32F (parental, undifferentiated)

value: iPSC 32F parental

value: Sullivan Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)

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


title: STAMP_18

source_name: hESC H1 treated with BMP4 for 120h

value: BMP4 treated hEST H1


title: WJL4194_RLF_N034

description:
Library name: WJL4194
Jkappa1 coding end bait

value: bone marrow

value: pro-B cells


title: WJL4195_RLF_N034

description:
Library name: WJL4195
Jkappa1 coding end bait


title: Medalist trial patient Responderj1383_samp33

description: Library name: j1383_samp33


title: Acep_For_2

description: Library name: Acep_For_2


title: Acep_For_3

description: Library name: Acep_For_3


title: Acep_For_4

description: Library name: Acep_For_4


title: STAMP_17

source_name: hESC H1 treated with BMP4 for 0h

value: Fixed cells

value: CosMx Human Universal Cell Characterization RNA Panel:1000


title: Medalist trial patient Responderj1383_samp35

description: Library name: j1383_samp35


title: Medalist trial patient Responderj1383_samp31

description: Library name: j1383_samp31


title: WJL4192_RLF_N034

description:
Library name: WJL4192
Jkappa1 coding end bait

source_name: vAbl-ProB

value: vAbl-ProB


title: Medalist trial patient Responderj1383_samp23

description: Library name: j1383_samp23


title: Acep_For_1

description: Library name: Acep_For_1

source_name: antennae


title: STAMP_15

source_name: Differentiated iPSC 32F to Ectoderm

value: Differentiated iPSC 32F

value: Polo Lab (Adelaide Centre for Epogenetics, The University of Adelaide, Monash University)

value: Single Molecule Imager


title: STAMP_16

source_name: Differentiated iPSC 32F to Endoderm


title: WJL4191_RLF_N034

description:
Library name: WJL4191
Jkappa1 coding end bait

value: p53-/- Setx deletion exon 14 Xlf-/-


title: STAMP_19

source_name: hESC H1 treated with BMP4 for 12h


title: STAMP_14

source_name: PBMC, MCF-7

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

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


title: Acep_DW_5

description: Library name: Acep_DW_5

value: antennae


title: Medalist trial patient Responderj1383_samp21

description: Library name: j1383_samp21

value: BMMNCs

value: Luspatercept


title: WJL4190_RLF_N034

description:
Library name: WJL4190
Jkappa1 coding end bait

value: p53-/- Setx deletion exon 3 Xlf-/-


title: Acep_DW_4

description: Library name: Acep_DW_4


title: Medalist trial patient Responderj1376_samp8

description: Library name: j1376_samp8


title: STAMP_12

source_name: PBMC

value: Blood

value: STEMCELL Technologies

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


title: Acep_DW_3

description: Library name: Acep_DW_3


title: WJL4189_RLF_N034

description:
Library name: WJL4189
Jkappa1 coding end bait

value: pro-B cells


title: Medalist trial patient Responderj1376_samp7

description: Library name: j1376_samp7


title: WJL4188_RLF_N034

description:
Library name: WJL4188
Jkappa1 coding end bait


title: Acep_DW_2

description: Library name: Acep_DW_2


title: STAMP_11

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)

value: Fixed cells


title: Acep_DW_1

description: Library name: Acep_DW_1


title: Medalist trial patient Responderj1376_samp5

description: Library name: j1376_samp5


title: WJL4186_RLF_N034

description:
Library name: WJL4186
Jkappa1 coding end bait

value: vAbl-ProB

value: p53-/- Setx deletion exon 14


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

city: Glasgow

first: Tyler

last: Stevenson

address: Jarret Building

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

institute: University of Glasgow

description: Library name: Hamster Am 141

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

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

value: Amygdala

value: Long 16L Photoperiod