title: Scan 35

value: Normal pancreas

value: St. Jude Children's Research Hospital


title: HMC3, co-culture, Rapamycin-treated, replicate 3

status: Public on Jul 28 2025

type: SRA

city: Freiburg

first: Michael

last: Schulz

address: Breisacher Straße 64

department: Institute for Neuropathology

country: Germany

institute: University Hospital Freiburg

description:
13_ZEINERetAl
col F
ZeinerEtAl_allSamples.csv

library_source: transcriptomic

data_processing:
FastQC Analysis
quality score filtering, poly-A trimming, artifact removal, removal of ‘N’ containing reads and clearing of rRNA contamination using a pipeline provided by the HUSAR platform, DKFZ.
Transcriptomes were mapped to the human genome using the genecode annotations (release v. 32; genome assembly version GRCh38.p13) and TopHat2 (v. 2.0.14)
The number of reads per gene was determined using HTSeq count.
Paired differential analysis was performed using   ‘DESeq2’  (version 1.18.1)
Assembly: Transcriptomes were mapped to the human genome using the genecode annotations (release v. 32; genome assembly version GRCh38.p13) and TopHat2 (v. 2.0.14)
Supplementary files format and content: .csv; processed data file contains annotated ENSEMBL IDs and gene names as well as readcounts which were annotated from HTSeq counts

molecule: total RNA

organism: Homo sapiens

source_name: HMC3 microglia cell line

growth_protocol: Cells were cultured in Dulbecco’s modified eagle medium (DMEM) containing 100 IU/ml penicillin and 100 mg/ml Streptomycin and 10% fetal calf serum (fcs)

extract_protocol:
Samples were washed with PBS and resuspended in TRIzol, and stored at -80 °C until further usage. RNA was isolated according to manufacturers instructions.
RNA-sequencing libraries were generated with the SMART-Seq preparation kit (CloneTech) and fragmented with the Nextera XT kit (Illumina).

treatment_protocol: Transwell co-cultivation of the human MG cell lines C20 or HMC3 with the glioma cell line LNT-229 was performed using 6- or respective 24-well cell culture inserts (1 μm pore). 6-well inserts were used for RNA analyses. MG were seeded into the lower chamber (6- well: 500.000/well, 24-well: 120.000/well) and glioma cells into the inserts (6-well insert: 400.000/well, 24-well insert: 30.000/well) separately in DMEM with 10% fcs 24 h prior to co-cultivation. To provide a MG monoculture control condition, C20 or HMC3 MG were seeded into the inserts and lower chambers. Cultivation was performed in serum-free DMEM with a total volume of 3 ml/500 μl or 2 ml/200 μl added to the well and insert (6-/24-well plate, respectively). Cultured cells were treated with the mTOR inhibitors 100 nM rapamycin and 100 nM torin2 as well as 400 μM temozolomide or corresponding vehicle controls for 24 h. Afterwards, C20 or HMC3 cells in the lower chamber were harvested for further RNA-Seq analysis.

tag: cell line

value: HMC3 microglia cell line

tag: cell type

value: microglia

tag: culture condition

value: co-culture with LNT-229 glioma cell line

tag: treatment

value: rapamycin


title: 44023_OB_6_2_TST_A11

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description: Library name: 44023_Exp185_OB_6_2_TST_A11

data_processing:
RNA-seq data was analyzed using the seq2science  pipeline which can be found at: https://github.com/vanheeringen-lab/seq2science (van der Sande M, Frölich S, Schäfers T, Smits JGA, Snabel RR, Rinzema S, van Heeringen SJ. 2023. Seq2science: an end-to-end workflow for functional genomics analysis. PeerJ 11:e16380 https://doi.org/10.7717/peerj.16380)
Assembly: GRCh38
Supplementary files format and content: .tsv file with read counts per gene: GRCh38-counts.tsv

source_name: blood

growth_protocol: Primary cells

extract_protocol:
At day 6, cells were harvested by scraping, centrifuged, and resuspended in 350 μl of Lysis Buffer RA1 from the NucleoSpin RNA kit (Macherey-Nagel) and saved at -80°C until RNA isolation. RNA was isolated using the NucleoSpin RNA kit following the manufacturer’s instructions.
Total RNA was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems). Oligo hybridization and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94°C for 6 min. First strand synthesis, second strand synthesis and A-tailing was performed according to the protocol. For the adaptor ligation, a 1.5 µM stock was used (NextFlex DNA barcodes, Bio Scientific). First and second post-ligation cleanup was performed according to protocol. A total of 11 PCR cycles were performed for library amplification. The library amplification cleanup was done using a 0.8x followed by a 1.0x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer kit, and the library concentration was measured using the dsDNA High Sensitivity Assay (Denovix). Paired-end sequencing of reads of 50 bp were generated using an Illumina NextSeq 500.

treatment_protocol: Adherent PBMCs of 5 healthy individuals were trained with 5 μg/mL BCG, 50 µM testosterone (TST, dissolved in ethanol), both or control (EtOH) according to in vitro trained immunity protocols.

tag: tissue

value: blood

value: monocyte

value: TST


title: LSC_Sub1_2

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

country: China

institute: Chongqing Medical University

library_source: genomic

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
The CUT&Tag assay was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein) according to the manufacturer’s protocol. 2,000-5,000 HSCs were harvested and resuspended in 45 µL wash buffer. Then 6 µL ConA beads were added to the sample and incubated at 37°C for 10 min. Then the supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL antibody buffer (20 mM Hepes, pH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1× PIC).
Then, 0.5 µL antibody was added to the sample and incubated at 4°C overnight. The supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL secondary antibody buffer, containing 0.5 µL goat anti-rabbit IgG antibody. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL ChiTag Buffer, containing 0.5 µL ChiTag transposome. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL tagmentation buffer. Then, 1 µL 10% SDS was added to the sample and incubated at 55°C for 10 min, and DNA was extracted using 2×DNA clean beads (Vazyme) and amplified with i5 and i7 primers (Vazyme) by 17-20 PCR cycles. The libraries were purified by 1.2×DNA clean beads (Vazyme).

treatment_protocol: HSCs (CD48-CD150+LSK) from Nup214fl/+ mice and LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Nup214fl/+ mice were sorted, followed by Sub1-CUT&Tag-seq

value: Bone marrow

value: Hematopoietic stem cell

tag: genotype

tag: cut&tag antibody

value: Sub1 (A7070,Abclonal)


title: HMC3, mono-culture, Vehicle-treated, replicate 2

description:
12_ZEINERetAl
col T
ZeinerEtAl_allSamples.csv

value: mono-culture with HMC3

value: vehicle


title: LSC_Sub1_1


title: Scan 34

type: RNA

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

country: USA

institute: St. Jude Children's Research Hospital

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

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

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

source_name: Normal pancreas

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

tag: sample source

tag: sample processed

value: Weill Cornell Medical Center

tag: sample type

value: FFPE

tag: technology

value: Xenium


title: Scan 33

value: Normal pancreas


title: 44022_OB_5_2_EtOH_A10

description: Library name: 44022_Exp185_OB_5_2_EtOH_A10

value: EtOH


title: HMC3, mono-culture, Temozolomide-treated, replicate 2

description:
11_ZEINERetAl
col Q
ZeinerEtAl_allSamples.csv

value: HMC3 microglia cell line

value: temozolomide


title: HSC_Sub1_2


title: 44021_OB_4_1_BCGTST_A09

description: Library name: 44021_Exp185_OB_4_1_BCGTST_A09

value: BCG+TST


title: HMC3, mono-culture, Rapamycin-treated, replicate 2

description:
10_ZEINERetAl
col N
ZeinerEtAl_allSamples.csv

value: microglia

value: rapamycin


title: HMC3, co-culture, Vehicle-treated, replicate 3

description:
15_ZEINERetAl
col L
ZeinerEtAl_allSamples.csv

value: co-culture with LNT-229 glioma cell line


title: 44020_OB_3_1_BCGEtOH_A08

description: Library name: 44020_Exp185_OB_3_1_BCGEtOH_A08

value: blood

value: monocyte

value: BCG+EtOH


title: Scan 31

value: St. Jude Children's Research Hospital


title: HSC_Sub1_1

value: Bone marrow

value: Hematopoietic stem cell

value: Sub1 (A7070,Abclonal)


title: HMC3, co-culture, Vehicle-treated, replicate 2

description:
9_ZEINERetAl
col K
ZeinerEtAl_allSamples.csv

value: vehicle


title: Scan 32

value: Weill Cornell Medical Center

value: FFPE

value: Xenium


title: HSC_NUP214_2

treatment_protocol: HSCs (CD48-CD150+LSK) from Nup214fl/+ mice and LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Nup214fl/+ and Nup214fl/+,Tie2-Cre (Nup214-HET) AML mice were sorted, followed by NUP214-CUT&Tag-seq


title: HSC_NUP214_1


title: 44018_OB_1_1_EtOH_A06

description: Library name: 44018_Exp185_OB_1_1_EtOH_A06

value: EtOH


title: HMC3, co-culture, Rapamycin-treated, replicate 2

description:
7_ZEINERetAl
col E
ZeinerEtAl_allSamples.csv

value: HMC3 microglia cell line


title: HMC3, co-culture, Temozolomide-treated, replicate 2

description:
8_ZEINERetAl
col H
ZeinerEtAl_allSamples.csv

value: temozolomide


title: HET_LSC_NUP214_2


title: Scan 28

description: 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

source_name: Prostate cancer

value: Prostate cancer

value: University of Adelaide

tag: biological replicate (filename)

tag: replicate

tag: processed data file name


title: PD9, Colon mucosa, B hyo infecto

city: León

first: Lucía

last: Pérez-Pérez

address: C/ Pedro Cárdenes s/n

country: Spain

institute: Universidad de León

description: Library name: PD9

data_processing:
Reads quality was analysed using the FastQC v0.11.9 software
These raw reads were trimmed, filtered for those with a Phred quality score of at least 25, and all adapters were removed with FastP v0.23.2 software
Reads were aligned to the reference genome (Sus scrofa 11.1 -assembly GCF_000003025.6, ENSEMBL database, release 108-) using the HISAT2 v2.2.1 software with defaul parameters.
Read counts per gene were performed with FeatureCounts v2.0.6 software using the GTF annotation of the reference genome.
Assembly: Sus scrofa 11.1 -assembly GCF_000003025.6, ENSEMBL database, release 108-
Supplementary files format and content: SAF file. Raw gene count

organism: Sus scrofa

source_name: Colon mucosa

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 500 ng of RNA per sample was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA kit following manufacturer protocols.

treatment_protocol: The infected group was orally challenged for three consecutive days with 30 mL of broth containing B. hyodysenteriae B-204 (ATCC 31212) strain at a concentration of 5 × 10^8 bacteria/mL.

value: Colon mucosa

value: Infected


title: Scan 29


title: HMC3, mono-culture, Vehicle-treated, replicate 1

description:
6_ZEINERetAl
col S
ZeinerEtAl_allSamples.csv

value: microglia

value: mono-culture with HMC3


title: HMC3, mono-culture, Temozolomide-treated, replicate 1

description:
5_ZEINERetAl
col P
ZeinerEtAl_allSamples.csv


title: HET_LSC_NUP214_1


title: PD8, Colon mucosa, B hyo infecto

description: Library name: PD8


title: PD7, Colon mucosa, B hyo infecto

description: Library name: PD7


title: Scan 26

source_name: Breast cancer

value: Breast cancer

value: Garvan Institute of Medical Research


title: FL_LSC_NUP214_2

value: Bone marrow

value: Hematopoietic stem cell


title: HMC3, mono-culture, Rapamycin-treated, replicate 1

description:
4_ZEINERetAl
col M
ZeinerEtAl_allSamples.csv

value: rapamycin


title: 44019_OB_2_1_TST_A07

description: Library name: 44019_Exp185_OB_2_1_TST_A07

value: blood

value: monocyte

value: TST


title: PD6, Colon mucosa, B hyo infecto

description: Library name: PD6


title: HMC3, co-culture, Vehicle-treated, replicate 1

description:
3_ZEINERetAl
col J
ZeinerEtAl_allSamples.csv

value: co-culture with LNT-229 glioma cell line

value: vehicle


title: Scan 27

value: FFPE

value: Xenium


title: FL_LSC_NUP214_1


title: HMC3, co-culture, Temozolomide-treated, replicate 1

description:
2_ZEINERetAl
col G
ZeinerEtAl_allSamples.csv

value: HMC3 microglia cell line

value: temozolomide


title: PD5, Colon mucosa, B hyo infecto

description: Library name: PD5

value: Colon mucosa

value: Infected


title: Scan 25

value: University of Adelaide


title: Scan 24

value: Breast cancer


title: LSC_HET_5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments per kilobase per million (FPKM) estimation was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq (a Python framework to work with high-throughput sequencing data), and differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven Nup214fl/+ and Nup214fl/+,Tie2-cre (Nup214-HET) AML mice were sorted, followed by RNA-seq


title: LSC_HET_4


title: HMC3, co-culture, Rapamycin-treated, replicate 1

description:
1_ZEINERetAl
column D
ZeinerEtAl_allSamples.csv

value: microglia


title: LSC_HET_3

value: Bone marrow


title: Scan 23

value: Garvan Institute of Medical Research


title: PD3, Colon mucosa, B hyo infecto

description: Library name: PD3


title: RH30, sgRNA targeting MyoD, biological rep3

city: Charleston

first: Denis

middle: C

last: Guttridge

state: SC

address: 173 Ashley Ave

department: Pediatrics

institute: Medical University of South Carolina

data_processing:
Basecalls were performed using bcl2fastq v2.20 with default settings. Read quality was assessed using FASTQC.
ATAC-seq reads were aligned to the UCSC hg38 genome using Rsubread. Proper pairs were identified with GenomicsAlignments Package
Blacklisted regions of the genome were excluded using the DAC exclusion list regions of the hg38 human reference genome (ENCSR636HFF).
To create ATAC-seq coverage plots, reads were normalized to reads per million mapped reads and reformatted in the bigWig file format.
Peaks were called uing MACS2
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

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

extract_protocol:
2x10^6 cells were frozen in 10% DMSO containing media and processed by QuickBiology (Monrovia, CA) following standard ATAC-seq protcols.
Libraries were prepared by QuickBiology (Monrovia, CA) with Nextera Tn5 transposase, amplified, assessed for quality control, and sequenced with Illumina High-throughput sequencing, with >60 million total reads of paired-end sequencing at 75-150 bp range.

treatment_protocol: Cells were transduced with Cas9 and sgRNA non targeting scramble guides or sgRNAs which targeted MyoD for CRISPR/Cas9 gene editing

value: Rhabdomyosarcoma

value: sgRNA targeting MyoD


title: LSC_HET_2

value: Hematopoietic stem cell


title: PD2, Colon mucosa, B hyo infecto

description: Library name: PD2


title: RH30, sgRNA targeting MyoD, biological rep2


title: PD1, Colon mucosa, B hyo infecto

description: Library name: PD1


title: LSC_HET_1


title: PD4, Colon mucosa, B hyo infecto

description: Library name: PD4


title: Retina, Bmal1-mg/-mg, rep5

city: Saint Louis

first: Charles

middle: W.

last: Pfeifer

state: Missouri

address: 660 S. Euclid Ave., Campus Box 8096

department: Ophthalmology and Visual Sciences

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software with a maximum of one mismatch in the indexing read. RNA-Seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Raw gene counts were then filtered based on a ≥1 CPM threshold for (n-1) samples in a given condition
Next, a standard EdgeR-limma analysis of gene-level features was performed, defining significant up- or downregulated genes as a |fold-change| > 1.50 with a FDR < 0.05.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: Group_KO_MG_Group_WT_MG_Differential_Expression.tsv
Supplementary files format and content: Group_KO_Ret_Group_WT_Ret_Differential_Expression.tsv
Supplementary files format and content: all.gene_counts.tsv

source_name: Retina

extract_protocol:
For RNA-Sequencing of microglia and retinal cells, total RNA was isolated from flow-sorted cells using the RNeasy Plus Micro Kit (Qiagen). RNA quantity and integrity was determined using a 2100 Bioanalyzer and RNA Pico kit (Agilent Technologies). All samples (n = 9) contained 2.0 – 4.0ng RNA and had RIN > 8.0
Library preparation was performed by the Genome Technology Access Center (GTAC) through the McDonnell Genome Institute (MGI) with 1-2ng of total RNA per sample. Ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech). Fragments for RNA-Sequencing experiments were amplified and sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases

value: Retina

value: Non-microglia retina cells


title: LSC_FL_5


title: RH30, sgRNA scramble, biological rep3

value: sgRNA scramble


title: Microglia, Bmal1-mg/-mg, rep5

value: Microglia


title: PD16, Colon mucosa, B hyo infecto

description: Library name: PD16


title: Retina, Bmal1-mg/-mg, rep4


title: PD14, Colon mucosa, B hyo infecto

description: Library name: PD14


title: PD15, Colon mucosa, B hyo infecto

description: Library name: PD15


title: LSC_FL_3


title: RH30, sgRNA scramble, biological rep2


title: LSC_FL_4


title: Scan 22

value: Prostate cancer

value: St. Jude Children's Research Hospital

value: FFPE

value: Xenium


title: RH30, sgRNA scramble, biological rep1


title: Scan 30

value: Weill Cornell Medical Center


title: PD13, Colon mucosa, B hyo infecto

description: Library name: PD13

value: Colon mucosa

value: Infected


title: Microglia, Bmal1-mg/-mg, rep4


title: LSC_FL_2


title: Retina, Bmal1-mg/-mg, rep3


title: PBMC-NKT

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The raw sequencing data were processed and mapped to the human TCR reference genome (hg38) using the Cell Ranger VDJ software. The frequencies of the α or β chain recombination were plotted to identify the unique TCR repertoires in each cell population.
Assembly: hg38
Supplementary files format and content: Sample_filtered_contig_annotations.csv, high-level annotations of each high-confidence contigs from cell-associated barcodes of each sample
Supplementary files format and content: Sample_clonotypes.csv, high-level descriptions of each clonotype of each sample
Library strategy: TCR-seq

source_name: In vitro culture

extract_protocol:
scTCR-seq was utilized to study the TCR sequencing of Allo/15BCAR-NKT cells. Five different cell types were delivered to the UCLA TCGB Core for library construction and scTCR-seq.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: In vitro culture

value: NKT cell


title: PD12, Colon mucosa, B hyo infecto

description: Library name: PD12


title: Scan 21

value: University of Adelaide

value: EAP


title: RH30, sgRNA targeting MyoD, biological rep1

value: Rhabdomyosarcoma

value: sgRNA targeting MyoD


title: h18WMC

city: Pok Fu Lam

first: Peikai

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description: single-cell transcriptomics on the menisci of a human embryonic sample

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: meniscus

extract_protocol:
The dissected tissues were digested with 0.02% collagenase P (Roche 11213865001) for 45 min at 37C, followed by filtering through 40μm cell strainers. Single cells were encapsulated using 10X Genomics Chromium Single Cell Chip (10x genomics) with Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s instructions, and libraries were sequenced on  NovaSeq6000 (Illumina).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: meniscus

tag: gestation stage

value: 18 weeks

tag: gender

value: male

value: no treatment

tag: combined number_of_reads_in_this_sample

tag: num of_cells_detected_in_this_sample


title: h18WKJ

description: single-cell transcriptomics on the knee joints of a human embryonic sample

source_name: whole knee joint

value: whole knee joint


title: Microglia, Bmal1-mg/-mg, rep3

value: Retina

tag: cell type

value: Microglia


title: LSC_FL_1

value: Bone marrow

value: Hematopoietic stem cell


title: HET_5

treatment_protocol: HSCs (CD48-CD150+LSK) from Nup214fl/+ and Nup214fl/+,Tie2-cre (Nup214-HET) mice were sorted, followed by RNA-seq


title: PD11, Colon mucosa, B hyo infecto

description: Library name: PD11

value: Colon mucosa

tag: treatment


title: Retina, Bmal1-mg/-mg, rep2

tag: tissue

value: Non-microglia retina cells


title: HET_4

tag: genotype


title: PD10, Colon mucosa, B hyo infecto

description: Library name: PD10

value: Infected


title: h9W

value: 9 weeks

value: female


title: HET_3


title: Microglia, Bmal1-mg/-mg, rep2


title: PC9, Colon mucosa, B hyo non_infected

description: Library name: PC9


title: Retina, Bmal1-mg/-mg, rep1


title: h12WA

value: 12 weeks


title: HET_2


title: PC8, Colon mucosa, B hyo non_infected

description: Library name: PC8


title: 2172 PBS mock inoculated [scRNA-seq]

city: Hong Kong

first: Mark

last: Zanin

state: Pokfulam

address: 7 Sassoon Road

department: School of Public Health

description: Library name: 2172

data_processing:
Individual single cell cDNA libraries from each infected ferret were aligned to this custom reference genome and then aggregated without normalization using CellRanger (v7.0.0, 10X Genomics) for downstream quality control analysis in Seurat (v4.1.1).
Assembly: Custom reference genome including Mustela putorius furo genome (ASM1176430v1.1, RefSeq GCF_011764305.1) and individual influenza gene segments.
Supplementary files format and content: tab-separated values files and matrix files

organism: Mustela putorius furo

source_name: nasal turbinates

extract_protocol:
Cells were isolated from the collected tissues using a MACS Epidermis Dissociation Kit (Human) (Milltenyi) and a GentleMACS dissociator according to the manufacturer’s instructions. Dead cells were removed using the MACS Dead Cell Removal Kit (Milltenyi) according to the manufacturer’s instructions. Cells were counted and adjusted to achieve a targeted cell recovery of 10,000.
Cells were loaded into gel-in-emulsion (GEM) beads using a 10X Chromium Controller (10X Genomics, 1000204) and the Single Cell 3' GEM, Library & Gel Bead Kit v3 kit (10X Genomics, 1000075). After GEM loading, RNA was reverse transcribed, incorporating cell-specific oligonucleotide tags. GEMS were then disrupted and cDNA was amplified and used to create a cDNA library using library construction kits (10X Genomics, 1000075). cDNA libraries were then sequenced on an Illumina HiSeq sequencer with 100 bp length in the 5’ configuration. Library quality was assessed using the 2100 Bioanalyzer with the high sensitivity DNA kit (Agilent Technologies).

treatment_protocol: Ferrets were inoculated with 10^6 plaque forming units of virus in 0.5mL PBS (0.25mL per nostril) following light anesthesia with isoflurane. Mock-inoculated ferrets were inoculated with 0.5mL PBS (0.25mL per nostril).

value: nasal turbinates

value: wild type

value: PBS mock inoculation


title: Microglia, Bmal1-mg/-mg, rep1


title: PC2, Colon mucosa, B hyo non_infected

description: Library name: PC2


title: HET_1


title: Retina, Bmal1f/f, rep4


title: FL_5


title: PC16, Colon mucosa, B hyo non_infected

description: Library name: PC16


title: 2202 DE300 [scRNA-seq]

description: Library name: 2202

tag: sample group

value: AT

value: viral inoculation


title: Microglia, Bmal1f/f, rep4


title: h12WB

value: no treatment


title: 2201 DE300 [scRNA-seq]

description: Library name: 2201


title: PC15, Colon mucosa, B hyo non_infected

description: Library name: PC15


title: FL_4


title: 2200 DE300 [scRNA-seq]

description: Library name: 2200


title: FL_3


title: 2199 DE300 [scRNA-seq]

description: Library name: 2199


title: Microglia, Bmal1f/f, rep3


title: FL_2


title: PC12, Colon mucosa, B hyo non_infected

description: Library name: PC12


title: Retina, Bmal1f/f, rep2


title: 2198 DE213 [scRNA-seq]

description: Library name: 2198

value: not AT


title: FL_1


title: PC11, Colon mucosa, B hyo non_infected

description: Library name: PC11


title: Microglia, Bmal1f/f, rep2

value: Retina


title: KO_3

treatment_protocol: At 3 days after pIpC administration, HSCs (CD48-CD150+LSK) from Nup214fl/fl and Nup214fl/fl,Mx1-cre mice were sorted, followed by RNA-seq


title: PC13, Colon mucosa, B hyo non_infected

description: Library name: PC13


title: 2196 DE213 [scRNA-seq]

description: Library name: 2196


title: KO_2


title: Retina, Bmal1f/f, rep1


title: 2195 DE213 [scRNA-seq]

description: Library name: 2195


title: Microglia, Bmal1f/f, rep1

value: Microglia


title: KO_1

value: Bone marrow


title: FL_5

value: Hematopoietic stem cell


title: Recurrent liver tumor, post-Myc reactivation after long-term regression, replicate 3

city: pittsburgh

first: Huabo

last: Wang

state: PA

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

description: Library name: RT_3

data_processing:
nf-core 3.12.0
Reads were processed following the nf-core pipeline
Assembly: mm10
Supplementary files format and content: TPM file includes the normalized expression for each sample.

molecule: polyA RNA

source_name: Liver

growth_protocol: All animal studies were reviewed and approved by the University of Pittsburgh Institutional Animal Care and Use Committee. FVB/N-Tg(tetO-MYC)36aBop/J and LAP-tTA mice (B6.Cg-Tg[Cebpb-tTA]5Bjd/J) (The Jackson Laboratory)  were genotyped according to published protocols and as recommended by the vendor. Animals were housed and fed ad libitum except that drinking water contained doxycycline (100 μg/ml) unless otherwise stated. For tumor induction studies, six groups of 3–4-week-old male and female mice were provided with doxycycline-free water. Three and 7 days later (D3 and D7), well before the appearance of any tumors, two groups of mice were sacrificed. Liver samples were flash-frozen for molecular and biochemical analyses or used immediately for enzymatic and metabolic assays requiring fresh tissues. The remaining mice were maintained off doxycycline for a further 3–4 weeks by which time all had developed large and aggressive HCCs. One group was sacrificed and used to duplicate the above studies, and the remaining three groups were again provided doxycycline-containing drinking water to suppress Myc expression and initiate tumor regression. Regressing tumors were then sampled 3 and 7 days later (R3 and R7 groups), at which point they were at least 50% smaller. Doxycycline was maintained for an additional 2–3 months in the remaining group and was then again removed to induce recurrence.

extract_protocol:
liver and tumor RNAs (five samples per time point) were purified using RNA Easy columns (Qiagen, Inc., Valencia, CA). RNA concentrations were determined with a Nanodrop ND-1000 instrument (NanoDrop Technologies Inc., Wilmington, DE), and RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)
The Sample preparation was replicated using Illumina TruSeq Stranded mRNA kit (San Diego, CA). mRNA was used to generate poly-A+ libraries using oligo-dT beads following 2 rounds of poly-A selection

value: Liver

value: FVB/N-Tg(tetO-MYC)36aBop/J x LAP-tTA


title: anther at TCP stage for lncRNA seq 1

city: Guangzhou

first: Dong

last: Zhou

address: wushan street

institute: south china agricultural university

description: Library name: TCP_lncRNA_1

data_processing:
Clean reads were assembled to transcripts by StringTie (version 1.3.2) and the assembled transcripts were mapped to the reference genome (The Arabidopsis Information Resource (TAIR10), https://www.arabidopsis.org/)
The unannotated transcripts obtained were further screened based on their coding potential determined by Coding Potential Calculator (CPC, score<0), Coding-Non-Coding Index (CNCI, score<0), Pfam-scan (Pfam, E-value<0.001), and Coding Potential Assessment Tool (CPAT, score<0) to distinguish lncRNAs from protein-coding genes.
Raw reads of sRNA-seq were trimmed to remove the 3' adapter sequences and filtered by cutadapt (version 1.9.1).
Clean reads were mapped to the reference genome using ShortStack (version 3.4) with parameters ‘-bowtie_m 1000-ranmax 50-mmap u-mismatches 0’.
Assembly: Arabidopsis_thaliana.TAIR10.35.dna.toplevel
Supplementary files format and content: normalized bw files

organism: Arabidopsis thaliana

source_name: Anther

growth_protocol: The ecotype Columbia (Col-0) of Arabidopsis was used for anther collection. Seeds were sowed on fully imbibed nursery blocks and kept in a temperature-controlled growth room. The growth room was set to 22°C with a photoperiod of light: dark=16 h:8 h. Seedlings were then transferred to square flowerpots (5×5×7.7 cm3) with substrates mixed with pearlite, turf, and vermiculite (3:2:1) when about four true leaves had been formed. During the full flowering stage, unopened flowers of various sizes were stained with 4',6'-diamidino-2-phenylindole (DAPI) solution to determine the accurate developmental stage. Subsequently, Anthers were picked out from floral buds by dissecting the buds under an anatomic microscope.

extract_protocol:
Samples were grounded into fine powders in 1.5 mL tubes with steel beads in a freezing tissue grinder (Jingxin, Shanghai, China) at 50 Hz for 60 s. The total RNA in each sample was extracted using AG RNAex Pro Reagent (Accurate Biology, Changsha, China) following the manufacturer’s instructions. The integrity, purity, and concentration of total RNAs were detected by agarose gel electrophoresis and NanoDrop 2000 (Thermo Fisher Scientific, MA, USA).
Libraries from twelve samples for mRNA and lncRNA sequencing were constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® as the instruction manual described.

treatment_protocol: All anthers at the same stage were pooled in a 1.5 mL EP tube, frozen in liquid nitrogen, and stored at –75 °C for further RNA extraction. Three duplicates were collected from at least 20 plants each time.

value: Anther


title: anther at BCP stage for lncRNA seq 1

description: Library name: BCP_lncRNA_1


title: FL_4


title: 2191 DE558 [scRNA-seq]

description: Library name: 2191


title: anther at BCP stage for lncRNA seq 2

description: Library name: BCP_lncRNA_2


title: Recurrent liver tumor, post-Myc reactivation after long-term regression, replicate 1

description: Library name: RT_1


title: 2197 DE213 [scRNA-seq]

description: Library name: 2197


title: FL_3


title: 2190 DE558 [scRNA-seq]

description: Library name: 2190


title: Recurrent liver tumor, post-Myc reactivation after long-term regression, replicate 5

description: Library name: RT_5


title: Regressing liver tumor, Day 7 post-Myc suppression, replicate 5

description: Library name: R7_5

value: doxycycline (100 μg/ml) in drinking water


title: 2189 DE558 [scRNA-seq]

description: Library name: 2189


title: anther at BCP stage for lncRNA seq 3

description: Library name: BCP_lncRNA_3


title: Regressing liver tumor, Day 7 post-Myc suppression, replicate 4

description: Library name: R7_4


title: Recurrent liver tumor, post-Myc reactivation after long-term regression, replicate 4

description: Library name: RT_4


title: 2192 DE558 [scRNA-seq]

description: Library name: 2192


title: FL_2


title: Recurrent liver tumor, post-Myc reactivation after long-term regression, replicate 2

description: Library name: RT_2


title: FL_1


title: Retina, Bmal1f/f, rep3

value: Non-microglia retina cells


title: anther at UNM stage for lncRNA seq 2

description: Library name: UNM_lncRNA_2


title: 2193 DE256 [scRNA-seq]

description: Library name: 2193


title: LSC_5

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice and LSCs (Lin-Sca-1-c-Kit+CD16/32+CD34+) from MLL-AF9-driven AML mice were sorted, followed by RNA-seq

value: Leukemia stem cell

value: Wild-type


title: 2188 DE256 [scRNA-seq]

description: Library name: 2188

value: nasal turbinates

value: wild type


title: Regressing liver tumor, Day 7 post-Myc suppression, replicate 3

description: Library name: R7_3


title: anther at UNM stage for lncRNA seq 1

description: Library name: UNM_lncRNA_1


title: Regressing liver tumor, Day 7 post-Myc suppression, replicate 2

description: Library name: R7_2


title: 2187 DE256 [scRNA-seq]

description: Library name: 2187

value: AT


title: anther at UNM stage for lncRNA seq 3

description: Library name: UNM_lncRNA_3


title: Regressing liver tumor, Day 7 post-Myc suppression, replicate 1

description: Library name: R7_1


title: LSC_3


title: LSC_4


title: 2178 PBS mock inoculated

description: Library name: 2178

data_processing:
Sequencing read quality was assessed using fastqc
Reads were aligned to the ferret genome MusPutFur1.0.96 using STAR and BWA
Read counts were quantified using HTSEQ
Normalization and differential expression analysis were performed using limma-voom
Assembly: MusPutFur1.0.96
Supplementary files format and content: .txt file including FPKM for each sample

extract_protocol:
Cells were isolated from the collected tissues using a MACS Epidermis Dissociation Kit (Human) (Milltenyi) and a GentleMACS dissociator according to the manufacturer’s instructions. Dead cells were removed using the MACS Dead Cell Removal Kit (Milltenyi) according to the manufacturer’s instructions.
RNA libraries for RNAseq were prepared using Illumina TruSeq Stranded mRNA kits as per manufacturer's instructions.

value: PBS mock inoculation


title: anther at TCP stage for miRNA seq 3

description: Library name: TCP_microRNA_3


title: LSC_2


title: 2176 PBS mock inoculated

description: Library name: 2176


title: Regressing liver tumor, Day 3 post-Myc suppression, replicate 4

description: Library name: R3_4


title: 2174 PBS mock inoculated

description: Library name: 2174


title: anther at TCP stage for miRNA seq 2

description: Library name: TCP_microRNA_2


title: Regressing liver tumor, Day 3 post-Myc suppression, replicate 5

description: Library name: R3_5


title: Regressing liver tumor, Day 3 post-Myc suppression, replicate 3

description: Library name: R3_3


title: LSC_1


title: HSC_5


title: Regressing liver tumor, Day 3 post-Myc suppression, replicate 2

description: Library name: R3_2


title: 2201 DE300

description: Library name: 2201

value: viral inoculation


title: 2202 DE300

description: Library name: 2202


title: 2172 PBS mock inoculated

description: Library name: 2172


title: anther at BCP stage for miRNA seq 3

description: Library name: BCP_microRNA_3


title: Regressing liver tumor, Day 3 post-Myc suppression, replicate 1

description: Library name: R3_1


title: HSC_4


title: HSC_3


title: Liver tumor, Day 21–28 post-Myc induction, replicate 4

description: Library name: T_4


title: 2200 DE300

description: Library name: 2200


title: anther at TCP stage for miRNA seq 1

description: Library name: TCP_microRNA_1


title: anther at BCP stage for miRNA seq 2

description: Library name: BCP_microRNA_2


title: anther at tetrad stage for lncRNA seq 3

description: Library name: Tetrad_lncRNA_3


title: HSC_2


title: Liver tumor, Day 21–28 post-Myc induction, replicate 3

description: Library name: T_3


title: 2199 DE300

description: Library name: 2199


title: HSC_1


title: Liver tumor, Day 21–28 post-Myc induction, replicate 2

description: Library name: T_2


title: 2198 DE213

description: Library name: 2198


title: anther at UNM stage for miRNA seq 2

description: Library name: UNM_microRNA_2


title: 2197 DE213

description: Library name: 2197


title: Allo15MCAR-NKT

description: 10x Genomics

data_processing:
The raw sequencing data were processed and mapped to the mouse reference genome (GRCh38/hg38) using the Cell Ranger software.
Assembly: hg38
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells. barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell. features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: Day 14

extract_protocol:
Peritoneal cavity cells (the tumor site) harvested from experimental animals at week 4 were subjected to FACS sorting for isolating mouse CD45+ immune cells. Cells isolated from 10 experimental mice were combined for each group.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: Day 14

tag: cell line

value: Immune cells

value: Peritoneal fluid


title: Liver tumor, Day 21–28 post-Myc induction, replicate 1

description: Library name: T_1


title: Liver, Day 7 post-Myc induction, rep 5

description: Library name: D7_5


title: anther at UNM stage for miRNA seq 3

description: Library name: UNM_microRNA_3


title: MCAR-T

description: 10x Genomics


title: NT

description: 10x Genomics


title: 2196 DE213

description: Library name: 2196


title: Liver, Day 7 post-Myc induction, rep 4

description: Library name: D7_4


title: anther at UNM stage for miRNA seq 1

description: Library name: UNM_microRNA_1


title: Blank

description: 10x Genomics


title: anther at TCP stage for lncRNA seq 3

description: Library name: TCP_lncRNA_3


title: 2195 DE213

description: Library name: 2195


title: 2194 DE256

description: Library name: 2194


title: Liver, Day 7 post-Myc induction, rep 3

description: Library name: D7_3


title: anther at TCP stage for lncRNA seq 2

description: Library name: TCP_lncRNA_2


title: Liver, Day 7 post-Myc induction, rep 2

description: Library name: D7_2


title: 2193 DE256

description: Library name: 2193


title: anther at tetrad stage for miRNA seq 2

description: Library name: Tetrad_microRNA_2


title: KCB_D3_BiolRep2

city: West Lafayette

first: Brittany

middle: L.

last: Allen-Petersen

state: IN

address: 201 S. University St., HANS 215

institute: Purdue University

data_processing:
Data processing and analysis were done using Partek Flow software
Raw reads were trimmed for Nextera adapter (CTGTCTCTTATACACATCT), minimum length>20 and quality>20 using Cutadapt_4_2
Trimmed reads were aligned to mouse genome mm10 build using BWA-MEM with default parameters. Alignments were filtered for mitochondrial reads, PCR duplicates, MAPQ<20, singletons, not primary reads, blacklisted regions and chrY alignments
Filtered alignments were used for peak calling using MACS in 2 ways: ATACseq-mode wherein peaks were called in samples individually, and ChIPseq-mode wherein peaks were called by comparison between conditions (biological replicates were pooled for comparison)
Assembly: mm10
Supplementary files format and content: BigWig generation was done using deeptools bamCoverage with –CPM option

source_name: Pancreatic acinar cells

growth_protocol: Acinar cell clusters were cultured in a final concentration of 3.5mg/ml rat tail collagen with 1X Waymouth media. Acinar cell media consisted of 1XWaymouth media supplemented with 100ng/mL soybean tripsin inhibitor, 1ng/mL dexamethasone, 1% FBS, and 1% penicillin/streptomycin. Cells were incubated during respective timepoints at 37*C and 5% CO2.

extract_protocol:
Acinar cell clusters were isolated, cultured, and collected for downstream analysis per the published JOVE protocol by Fleming Martinez and Storz.
ATACseq libraries were constructed according to the Omni-ATAC protocol and then double size selection was performed according to a published protocol.

value: Pancreatic acinar cells

value: KCB

value: Differentiation time points D3


title: 2192 DE558

description: Library name: 2192


title: anther at tetrad stage for miRNA seq 1

description: Library name: Tetrad_microRNA_1


title: Liver, Day 3 post-Myc induction, rep 5

description: Library name: D3_5

value: Liver

value: FVB/N-Tg(tetO-MYC)36aBop/J x LAP-tTA


title: 2191 DE558

description: Library name: 2191


title: KCB_D3_BiolRep3


title: KCB_D2_BiolRep3

value: Differentiation time points D2


title: 2189 DE558

description: Library name: 2189


title: KCB_D2_BiolRep2


title: KCB_D2_BiolRep1


title: 2188 DE256

description: Library name: 2188


title: 2190 DE558

description: Library name: 2190


title: Liver, Day 3 post-Myc induction, rep 1

description: Library name: D3_1


title: anther at tetrad stage for lncRNA seq 1

description: Library name: Tetrad_lncRNA_1

value: Anther


title: Liver, Day 3 post-Myc induction, rep 2

description: Library name: D3_2


title: anther at tetrad stage for lncRNA seq 2

description: Library name: Tetrad_lncRNA_2


title: 2187 DE256

description: Library name: 2187


title: anther at BCP stage for miRNA seq 1

description: Library name: BCP_microRNA_1


title: Liver, Day 7 post-Myc induction, rep 1

description: Library name: D7_1


title: A_cas_untreated_EMseq

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Library name: A_cas_untreated_EMseq

data_processing:
The EM-seq libraries were sequenced at NovoGene, using Illumina NovaSeq6000 platform, aiming at coverages >30x for reference methylomes, and 5x for shallow treatment samples. The obtained FASTQ files were mapped to the reference genomes using BS-Seeker2, with BOWTIE2 as backend alignment tool. PCR duplicate reads were removed using Sambamba, and methylation calling was obtained using CGmapTools.
We used HISAT2 to map RNA-seq reads against the reference genomes, obtaining counts on transposable elements and protein-coding genes using the TElocal pipeline (https://github.com/mhammell-laboratory/TElocal).
Assembly: The chromosome-scale genome and annotation for Acanthamoeba castellanii Neff strain was obtained from https://zenodo.org/records/6800059. The genome for Cyanophora paradoxa was downloaded from http://cyanophora.rutgers.edu/cyanophora_v2018/blast.php. The genome of Naegleria gruberi was downloaded from GitHub: https://github.com/AlexdeMendoza/6mA_evolution/tree/main/Genomes.
Supplementary files format and content: The EM-seq is presented as CGmap files, described in: https://github.com/BSSeeker/BSseeker2. The RNA-seq file are counts on genes and transposable elements for each sample as obtained by TElocal.
Library strategy: EM-seq

organism: Acanthamoeba castellanii

source_name: axenic cell culture

growth_protocol: A. castellanii Neff strain was grown at 23°C in ATCC medium (712 PYG), using 100 mL ventend flasks. N. gruberi NEG-M was grown at 30°C in 1034 Modified PYNFH medium. DNA from untreated cultures of A. castellanii and N. gruberi were kindly provided by Meritxell Antó of Ruiz-Trillo Lab, Institut de Biología Evolutiva, Barcelona. Purified genomic DNA from Cyanophora paradoxa was purchased from CCAP collection.

extract_protocol:
DNA from drug-treated cultures were extracted using the NEB Monarch Genomic DNA Purification Kit. Total RNA from these cultures were extracted using the Monarch Total RNA Miniprep Kit.
For each library, 100-200 ng of initial gDNA were spiked in with unmethylated lambda genome control and methylated pUC19 plasmid control. These were sheared to 300 bp using a Covaris sonicator, and then used as input for Enzymatic Methyl-Seq kit (New England Biolabs), following manufacturer instructions. We used 200 ng of RNA from treated samples to build mRNA-seq libraries, first enriching for poly-A transcripts with the NEB Magnetic mRNA Isolation Kit S1550S, and then building the libraries with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760L) according to manufacturer's instructions.

treatment_protocol: DNA demethylation drugs 5-Azacytidine (ab142744 Abcam), decitabine (ab120842), and zebularine (ab141264) were dissolved in DMSO as per manufacturer’s instructions. A. castellanii was grown with 0 M, 10 nM, 100 nM, 1 µM, 10 µM, and 100 µM final concentration of each drug in 4ml ATCC (712 PYG) 1% DMSO media in a 6 well plate, and effects were tracked daily for 5 days, in duplicate. No treatments displayed a growth phenotype. A. castellanii DNA and RNA were extracted from cultures grown for 4 days in 3.5 mL ATCC (712 PYG) 1% DMSO media, with or without their respective drug in triplicate, at a final drug concentration of 100µM. N. gruberi DNA and RNA were extracted from cultures grown under the same conditions, with 1034 Modified PYNFH media.

value: axenic cell culture

value: Neff

value: Trophozoite

value: No treatment


title: KCB_D1_BiolRep3

value: Differentiation time points D1


title: A_cas_RNA_DMSO_3

description: Library name: A_cas_RNA_DMSO_3

data_processing:
The EM-seq libraries were sequenced at NovoGene, using Illumina NovaSeq6000 platform, aiming at coverages >30x for reference methylomes, and 5x for shallow treatment samples. The obtained FASTQ files were mapped to the reference genomes using BS-Seeker2, with BOWTIE2 as backend alignment tool. PCR duplicate reads were removed using Sambamba, and methylation calling was obtained using CGmapTools.
We used HISAT2 to map RNA-seq reads against the reference genomes, obtaining counts on transposable elements and protein-coding genes using the TElocal pipeline (https://github.com/mhammell-laboratory/TElocal).
Assembly: The chromosome-scale genome and annotation for Acanthamoeba castellanii Neff strain was obtained from https://zenodo.org/records/6800059. The genome for Cyanophora paradoxa was downloaded from http://cyanophora.rutgers.edu/cyanophora_v2018/blast.php. The genome of Naegleria gruberi was downloaded from GitHub: https://github.com/AlexdeMendoza/6mA_evolution/tree/main/Genomes.
Supplementary files format and content: The EM-seq is presented as CGmap files, described in: https://github.com/BSSeeker/BSseeker2. The RNA-seq file are counts on genes and transposable elements for each sample as obtained by TElocal.

value: DMSO 1% control


title: Scan 20

tag: tissue type

value: Prostate cancer

tag: sample source

value: University of Adelaide

value: Weill Cornell Medical Center

value: FFPE

value: CosMx


title: Control Liver, rep 5

description: Library name: Liver_5

value: doxycycline (100 μg/ml) in drinking water


title: KCB_D3_BiolRep1

value: Pancreatic acinar cells

value: KCB

value: Differentiation time points D3


title: A_cas_RNA_DMSO_2

description: Library name: A_cas_RNA_DMSO_2


title: Liver, Day 3 post-Myc induction, rep 4

description: Library name: D3_4

value: Liver

value: FVB/N-Tg(tetO-MYC)36aBop/J x LAP-tTA


title: KCB_D1_BiolRep1


title: Scan 19

value: Normal pancreas

tag: sample processed

tag: sample type


title: Liver, Day 3 post-Myc induction, rep 3

description: Library name: D3_3


title: KC_D3_BiolRep3

value: KC


title: Control Liver, rep 3

description: Library name: Liver_3


title: A_cas_RNA_Dec_3

description: Library name: A_cas_RNA_Dec_3

value: axenic cell culture

value: Neff

value: Trophozoite

value: Decitabine 100µM + DMSO


title: Control Liver, rep 2

description: Library name: Liver_2


title: A_cas_RNA_Dec_2

description: Library name: A_cas_RNA_Dec_2


title: Scan 16

tag: biological replicate (filename)

tag: technology


title: KCB_D1_BiolRep2

value: Differentiation time points D1


title: Control Liver, rep 1

description: Library name: Liver_1


title: A_cas_RNA_Dec_1

description: Library name: A_cas_RNA_Dec_1


title: x4391_meKO_chow

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: Library name: 4391

data_processing:
The gene counts were normalized by rlog transformation and analyzed by the DeSeq2 pipeline.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: macrophages

extract_protocol:
Trizol
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: 8 week old mice (8 WT, 8 meKO) were injected with AAV8PCSK9 to remove LDL receptor from hepatocytes.  Combined with a high fat ("Western") diet, these animals become hypercholesterolemic.  4 WT and 4 meKO animals were fed the high fat diet; control animals (r of each genotype) remained on a chow diet.

value: macrophages

value: meKO

value: chow


title: KC_D2_BiolRep3

value: Differentiation time points D2


title: A_cas_RNA_Aza_3

description: Library name: A_cas_RNA_Aza_3

value: 5-Azacytidine 100µM + DMSO


title: Control Liver, rep 4

description: Library name: Liver_4

value: doxycycline (100 μg/ml) in drinking water


title: A_cas_RNA_DMSO_1

description: Library name: A_cas_RNA_DMSO_1

value: DMSO 1% control


title: KC_D2_BiolRep2

value: Pancreatic acinar cells


title: Scan 14

value: Weill Cornell Medical Center

value: FFPE

tag: replicate

value: CosMx

tag: processed data file name


title: A_cas_RNA_Aza_2

description: Library name: A_cas_RNA_Aza_2


title: Scan 18

value: Normal pancreas


title: x4370_meKO_chow

description: Library name: 4370


title: Scan 13


title: KC_D3_BiolRep2

value: KC

value: Differentiation time points D3


title: KC_D2_BiolRep1


title: KC_D1_BiolRep3


title: A_cas_RNA_Aza_1

description: Library name: A_cas_RNA_Aza_1

value: axenic cell culture

value: Neff

value: Trophozoite


title: KC_D3_BiolRep1


title: Scan 17


title: x4357_meKO_HFD

description: Library name: 4357

value: macrophages

value: HFD


title: Scan 12


title: A_cas_EMseq_Zeb_3

description: Library name: A_cas_EMseq_Zeb_3

value: Zebularine 100µM + DMSO


title: x4354_WT_HFD

description: Library name: 4354

value: WT


title: KC_D1_BiolRep2

value: Differentiation time points D1


title: Scan 15


title: Scan 11


title: x4390_meKO_HFD

description: Library name: 4390

value: meKO


title: A_cas_EMseq_Zeb_2

description: Library name: A_cas_EMseq_Zeb_2


title: x4353_WT_chow

description: Library name: 4353

value: chow


title: Scan 10


title: KC_D1_BiolRep1

value: Pancreatic acinar cells


title: KC_D1_3

data_processing:
Datasets were trimmed with fastp (v0.23.2) to remove adapter sequences and low quality bases with a score less than Q30. Remaining reads with lengths greater than 50bp post trimming were carried forward.
Trimmed reads were aligned to the Mus musculus reference genome (GRCm39) from Ensembl release 109 using STAR Aligner version 2.7.4a in two pass mode
featureCounts (v1.6.1) was used in paired-end mode to quantify genes in unstranded fashion
edgeR (version 3.36.0), under R (version 4.1.3) was used for pair-wise comparisons; maSigPro (version 1.66.0) was used for time-series analyses. Samples from Day1 were taken as reference
Assembly: GRCm39
Supplementary files format and content: Counts matrix containing the gene quantifications from all the samples, processed with featureCounts

extract_protocol:
Acinar cell clusters were isolated, cultured, and collected for downstream analysis per the published JOVE protocol by Fleming Martinez and Storz.
RNA was isolated using the ThermoScientific GeneJET Purification Kit (Thermofisher, #K0732). mRNA was polyA enriched and RNA-seq libraries were generated and Illumina sequenced by Novogene.


title: A_cas_EMseq_Zeb_1

description: Library name: A_cas_EMseq_Zeb_1


title: x4352_WT_HFD

description: Library name: 4352


title: Scan 9

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.

value: Weill Cornell Medical Center


title: Scan 8

value: FFPE


title: x4351_WT_chow

description: Library name: 4351


title: A_cas_EMseq_DMSO_3

description: Library name: A_cas_EMseq_DMSO_3

value: DMSO 1% control


title: x4348_WT_HFD

description: Library name: 4348


title: Scan 7

value: Prostate cancer

value: University of Adelaide

value: CosMx


title: A_cas_EMseq_DMSO_2

description: Library name: A_cas_EMseq_DMSO_2

value: axenic cell culture


title: Scan 6


title: KC_D2_3

value: KC

value: Differentiation time points D2


title: A_cas_EMseq_DMSO_1

description: Library name: A_cas_EMseq_DMSO_1

value: Neff

value: Trophozoite


title: KC_D2_2


title: x4343_meKO_chow

description: Library name: 4343

value: macrophages


title: x4334_WT_chow

description: Library name: 4334

value: WT


title: KC_D2_1


title: A_cas_EMseq_Dec_2

description: Library name: A_cas_EMseq_Dec_2

value: Decitabine 100µM + DMSO


title: KC_D3_3

value: Differentiation time points D3


title: Scan 5

value: Breast cancer

value: Garvan Institute of Medical Research


title: A_cas_EMseq_Dec_1

description: Library name: A_cas_EMseq_Dec_1


title: x4332_meKO_HFD

description: Library name: 4332

value: meKO

value: HFD


title: Scan 4

value: FFPE


title: A_cas_EMseq_Aza_3

description: Library name: A_cas_EMseq_Aza_3

value: 5-Azacytidine 100µM + DMSO


title: KC_D1_1

value: Pancreatic acinar cells

value: Differentiation time points D1


title: NvO_HypoThy-PGE.2

city: Dallas

first: Nicolai

middle: S

last: van Oers

state: TX

address: NA2.200, 6000 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: 28bp Read1, 8bp Index, 98bp Read2

data_processing:
BCL files were demultiplexed using cellranger(v5.0.1)
Alignment, barcode counting, UMI counting were performed using cellranger(v5.0.1)
PCA, clustering, and differential expression was performed using Seurat
Assembly: mm10
Supplementary files format and content: count matrix in a sparse matrix format
Supplementary files format and content: barcode id of the sample
Supplementary files format and content: gene ids of the sample

source_name: E13-13.5 thymus

extract_protocol:
Fetal thymic lobes were isolated at E13-13.5 gestational age. Fetal lobes were subjected to trypsin digestion to obtain single cells.
Caitlin/Vanessa- McDermott Center at UT Southwestern Medical Center

value: E13-13.5 thymus


title: A_cas_EMseq_Aza_2

description: Library name: A_cas_EMseq_Aza_2

value: axenic cell culture


title: NvO_HypoThy-Minox

description: 28bp Read1, 8bp Index, 98bp Read2

value: Minoxidil


title: Scan 3

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

value: University of Adelaide

value: CosMx


title: Scan 2


title: KC_D3_1

value: KC


title: A_cas_EMseq_Aza_1

description: Library name: A_cas_EMseq_Aza_1

value: Neff

value: Trophozoite


title: NvO_HypoThy-ETOH

description: 28bp Read1, 8bp Index, 98bp Read2

value: ETOH


title: Scan 1

value: Prostate cancer

value: St. Jude Children's Research Hospital


title: KCBKO_D3_2

value: KCB

value: Differentiation time points D3


title: C_par_untreated_EMseq

description: Library name: C_par_untreated_EMseq

organism: Cyanophora paradoxa

value: CCAP 981

value: Normal cell culture

value: No treatment


title: KCBKO_D3_3

value: Pancreatic acinar cells


title: strain 1cA640V-1, biological replicate 3

first: Katherine

last: Barker

address: 262 Danny Thomas Place, Mail Stop 313, Room I5200

department: Pharmacy & Pharmaceutical Sciences

description: Library name: 2327317_ksb015

data_processing:
Data were analyzed using the Galaxy web platform public server at usegalaxy.org.
Read quality was assessed and reads were quality-trimmed with a PHRED cutoff of 20 using FastP.
Reads were then mapped to the C. auris B8441 reference assembly (NCBI GCA_002759435.2) using RNA Star with default parameters followed by quantification using featureCounts and assessment of differential expression using DESeq2.
Transcriptional overlap between strains was assessed using either UpsetR R Package or DiVenn 2.0.
Assembly: GCA_002759435.2
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Candidozyma auris

source_name: fungal strain

growth_protocol: For RNA isolation an aliquot of cells from an overnight culture of each strain was used to inoculate 10 ml MOPS-buffered RPMI + 2% glucose (pH 7.0) to a OD600=0.08-0.12, and the diluted culture was incubated at 35degC in a shaking incubator (220 rpm) until it reached mid-log phase (6 hrs).

extract_protocol:
Cells were collected by centrifugation, supernatants removed, and the cell pellets stored at -80degC until RNA isolation. Cell cultures were grown in triplicate. Cell pellets were thawed and resuspended in 100 µl FE Buffer (98% formamide, 0.01 M EDTA) at room temperature. Fifty microliters of 1 mm RNase-free glass beads was added, and the cells were disrupted in a vortex disruptor for 5 min at room temperature followed by snap-cooling on ice. The cell lysate was centrifuged to remove cell debris, and the crude RNA extract collected from the supernatant. The extract was DNase-treated for 30 min and precipitated by isopropanol precipitation. RNA integrity was confirmed through agarose gel electrophoresis using the bleach gel method, and concentrations were approximated by Nanodrop.
RNA sequencing was performed using Illumina NextSeq for stranded mRNA. Libraries were prepared with paired-end adapters using Illumina chemistries per manufacturer’s instructions, with read lengths of approximately 150 bp with at least 50 million raw reads per sample.

value: fungal strain


title: donor3_Cas9

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Library name: Gen-EBES1_12RNA

data_processing:
Read quality was assessed using FastQC [version 0.11.9]. Adapter sequences and low-quality bases (Q < 20) were trimmed from raw reads with BBDuk [version 38.92]; moreover, the first 10 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp post-trimming were discarded.
Trimmed reads were aligned to the human reference genome (hg38) using STAR [version 2.7.9a]. Raw gene counts were generated in R-4.1.1 using the featureCounts function of the Rsubread package [version 2.8.1] and the GENCODE 44 basic gene annotation for hg38 reference genome.
Raw gene counts were normalized to counts per million mapped reads (CPM) and to fragments per kilobase of exon per million mapped reads (FPKM) using the edgeR R package [version 3.36.0]; only genes with a CPM greater than 1 in at least 3 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: FPKM obtained using edgeR

source_name: Bone marrow

growth_protocol: Cells were cultured in pre-activation medium for 48 h before electroporation and 48 h after the electroporation

extract_protocol:
Total RNA was isolated from control or edited bone marrow derived-SCD HSPCs using the quick-DNA/RNA miniprep kit (Zymo)
RNA-seq libraries were prepared starting from 30 ng to 50 ng of total RNA using Watchmaker RNA kit with Polaris Depletion - rRNA/Globin (HMR) as recommended by the manufacturer.

treatment_protocol: Cells were electroporated with a combination of base editors mRNA or Cas9 nuclease RNP and sgRNA targeting the+58-kb and the +55-kb enhancers of BCL11A, and then cultured for 2 additional days. Cells electroporated with TE buffer only were used as controls.

value: Bone marrow

value: SCD CD34+ HSPCs

value: SCD

value: electroporated with Cas9-nuclease RNP and GATA_bs_4 and ATF4_bs_4 sgRNA


title: KCBKO_D3_1


title: strain 1cA640V-1, biological replicate 2

description: Library name: 2327316_ksb014


title: znf706_CT_rep2

city: Beijing

first: Xiaotong

last: Wu

address: Haidian

institute: Tsinghua University

data_processing:
All reads were aligned to the zebrafish reference genome (danRer11) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters ?t ?q ?N 1 ?L 25. All unmapped reads, nonuniquely mapped reads, and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of RPKM. To visualize the signals in the UCSC Genome Browser, each read was extended by 250 bp, and the coverage for each base was counted. Peaks were called using MACS2 (Zhang et al., 2008) with the parameters -p1e-4 --nomodel -g 1.3e10.
Assembly: danRer11
Supplementary files format and content: bw

organism: Danio rerio

source_name: oocyte

extract_protocol: The operation from the anesthetization of adult fish to oocyte digestion is the same as that for RNA-seq. It is worth noting that CUT&Tag is a technique capturing genomic DNA, thus, it is imperative to eliminate the contamination from the granulosa cells and other somatic cells that envelop the oocytes. In our study, we performed the digestion by cell dissociation buffer (PCM, PC-33689) to get rid of somatic cells. The oocyte surface exhibits a pronounced smoothness, signifying the removal of somatic cells, which would be further validated by DAPI staining. Then, the medium containing the oocytes was drawn through a 100 ?m cell strainer using a pipette, followed by a 2-minute incubation period to allow for the gravitational sedimentation of the oocytes at the bottom of the plate. To remove impurities, the sample was thoroughly washed 2-3 times with a preheated L-15 medium. Approximately 5,000 WT stage I oocytes were collected, followed by library construction using the Hyperactive U  niversal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904) and sequencing (Novogene, Hiseq-PE150 platform). The primary antibody used in the experimental group is rabbit anti-Znf706 (Aviva, arp32987-P050, 2.5?g / 50?l), while rabbit anti-IgG antibody (Cell Signaling Technology, 2729s, 2.5 ?g / 50?l) in the control group. The secondary antibody was goat anti-rabbit IgG H&L (Abcam, ab6702, 1:100 dilution). The experimental group underwent two biological replicates.

value: oocyte

value: Wild type


title: KC_D3_2

value: KC


title: donor3_DBE

description: Library name: Gen-EBES1_11RNA

value: electroporated with TadDE mRNA and GATA_bs_1 and ATF4_bs_2 sgRNA


title: KCBKO_D2_3

value: Differentiation time points D2


title: NvO_NThy-ETOH

description: 28bp Read1, 8bp Index, 98bp Read2

value: E13-13.5 thymus

value: WT

value: ETOH


title: znf706_CT_rep1


title: KCBKO_D2_2

value: KCB


title: IgG_con


title: donor3_TE

description: Library name: Gen-EBES1_9RNA

value: electroporated with TE buffer only


title: strain 1cA640V-1, biological replicate 1

description: Library name: 2327315_ksb013


title: strain 1cA657V-7B1, biological replicate 3

description: Library name: 2327314_ksb012


title: donor2_Cas9

description: Library name: Gen-EBES1_8RNA


title: znf706_stageII_oocyte_rep2

data_processing:
RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low-quality reads.
The filtered data were then mapped to the zebrafish reference genome (danRer11) by STAR (version: STAR_2.5.3a_modified).
The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1).
Assembly: danRer11
Supplementary files format and content: tab-delimited ext file includes FPKM values for each samples
Supplementary files format and content: The RNA-seq data were first processed using Trim Galore! with default parameters to trim the adapter-containing and low-quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer11) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilter-MultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to FPKM values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).

extract_protocol:
In the context of the current investigation, a protocol for the isolation of oocytes from juvenile female fish was developed, aimed at maximizing yield and maintaining cellular integrity. The first step involved the euthanization of the WT and znf706-/- juvenile female fish (3-month-old) by submerging them in an ice-water mixture. After euthanization, the abdominal cavity of the fish was carefully opened using surgical scissors and the ovaries were bilaterally detached from the abdomen by utilizing forceps. The excised ovaries were promptly transferred into a 6-well plate preloaded with 2 ml digestive buffer (cell dissociation buffer, PCM, PC-33689) and incubated for 2-3 hrs at a temperature of 28.5℃. To enhance the efficacy of the digestive process, the 6-well plate was shaken every half hour during incubation. Once the digestion period was complete, the L-15 medium, which had been preheated to 28.5℃, was added to the digestive buffer to halt the digestion process effectively. To eliminate residual impurities, the oocytes were subjected to a series of washing steps involving the addition of fresh L-15 medium, followed by gentle resuspension of the oocytes, a process repeated 2-3 times to ensure thorough cleansing. Approximately 600 stage I oocytes and 150 stage II oocytes were collected manually with a pipette.
All the liquid nitrogen-freezing samples (stages I and II oocytes) were sent to Novogene for RNA-seq library preparation


title: KCBKO_D2_1


title: strain 1cA657V-7B1, biological replicate 2

description: Library name: 2327313_ksb011


title: znf706_stageII_oocyte_rep1


title: KCBKO_D1_2

value: Differentiation time points D1


title: anther at tetrad stage for miRNA seq 3

description: Library name: Tetrad_microRNA_3

value: Anther


title: donor2_DBE

description: Library name: Gen-EBES1_7RNA


title: donor3_CBE

description: Library name: Gen-EBES1_10RNA

value: electroporated with AncBE4max mRNA and GATA_bs_1 and ATF4_bs_2 sgRNA


title: KCBKO_D1_1

value: Pancreatic acinar cells