title: 3W, infected, day3

city: Wuhan

first: Xianliang

last: Ke

state: Hubei

address: No. 44, xiaohongshan street

institute: Wuhan Institute of Virology, Chinese Academy of Science

description: 10x genomics

data_processing:
Data processing: CellRanger takes FASTQ filesand performs alignment, filtering, barcode counting, and UMI counting to generate feature-barcoded matrices.
mm10 reference was built using 10xGenomics offered pre-built CellRanger reference package.
Assembly: mm10
Supplementary files format and content: tab-seperated value files and matrix files

source_name: lung

extract_protocol:
The whole lungs of three mice from each group were removed, washed in cold phosphate-buffered saline (PBS), and cut into small pieces using scissors. Subsequently, the dissected lungs were washed twice with DMEM and digested with Liberase TM (33.3 μg/mL, Sigma-Aldrich, USA) and DNaseI (133.3 ug/mL, Roche, USA) in 15 mL DMEM at 37 ℃ for 30 min with rotation. The reaction system was quenched by mixing the reaction system with 30 mL PBS supplemented with 2 % fetal bovine serum (FBS). Sequentially, cells were filtered through a 40-μm filter, pelleted by centrifugation at 500 x g for 8 min, resuspended in 5 mL red blood cell lysis buffer, and incubated at room temperature (~25 oC). After 5 min, the lysis reaction was stopped by adding 10 mL PBS with 2 % FBS. Cells were harvested by centrifugation at 500 × g for 8 min and resuspended in 200 μL PBS with 2 % FBS. After filtering through a 35-μm filter, cells were counted under a microscope and diluted to 1×106 cells. In total, 12,000 cells were loaded in the lane with 10x Chromium (10x Genomics, USA).
library construction was performed according to the manualfacter's instructions (Single cell 3' V2 kit, 10x genomics).

value: lung

value: immune cells

value: lung immune cells

tag: treatment

value: infected with 2.25E+06 pfu SARS-CoV-2 VIRUS


title: Starvation, high GFP population, rep 4

status: Public on Jun 30 2025

type: SRA

city: Ottawa

first: Truc

last: Losier

state: ON

address: 451 Smyth Road

department: CMM

country: Canada

institute: University of Ottawa

description: Library name: Sample 16

library_source: other

data_processing:
Sequencing was done on an Illumina Nextseq500 150 cycle high output kit, 150 bp single end reads with 8 bp dual indexes were performed.
Basecalling was performed by Illumina Real-Time Analysis (RTA v2)
FastQ generation was performed with Illumina bcl2fastq v2.20+
NGS results were analysed using CRISPRBetaBinomial.
Supplementary files format and content: csv files incude various metrics about the data quality (total read counts, mapped read counts, mappability, and coverage) and provide sgRNA- and gene-level summary statistics of the screens.
Library strategy: CRISPR Screen

molecule: other

organism: Homo sapiens

growth_protocol: HEK293A expressing DsRed-IRES-GFP-p62 reporter line were cultured in DMEM supplemented with 10% bovine calf serum (VWR Life Science Seradigm).

extract_protocol:
Genomic DNA of the sorted and unsorted fixed cells were then extracted using the protocol described previously. The sgRNA library was amplified by a two-step PCR protocol for NGS. All gDNA of sorted samples were used to maximize the representations. For the unsorted/bulk samples, 22890 ng of gDNA, which is relevant to 1250 x representation, was used for PCR1. PCR1 and PCR2 products were purified using AMPure XP Bead-Based Reagent (Beckman Coulter, A63881) according to manufacturer's instructions.
The CRISPR knockout pooled library was purchased from Addgene (Cat#1000000083) and amplified using the protocol provided by Addgene.

treatment_protocol: Media was changed 24 h before experiments. Amino acid starvation media was prepared based on Gibco standard recipe omitting all amino acids and supplemented as above without addition of non-essential amino acids and substitution with dialysed FBS (Invitrogen). Tunicamycin (10 µg/mL) or clofibrate (1 mM) was added to the cells for 6 hours. The untreated and treated cells were fixed with 2% PFA for 10 min at room temperature, followed by 15 min incubation with Tris (pH 8, direct addition to 2% PFA to create a final concentration of 1 M). Following aspiration of media, the cells were collected using scrapers, stored in ice-cold flow buffer (1% BSA and 2 mM EDTA in PBS), and filtered using cell strainers (70 µM, Falcon). The samples were then sorted into high and low GFP populations. These populations were then pelleted by centrifugation (4000 rpm for 10 min at 40C) and stored at -80C freezer for downstream analysis.

tag: cell line

tag: cell type

value: human embryonic kidney cells


title: 19M, infected, day3

country: China

description: 10x genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: age


title: STAMP_115

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.

molecule: total RNA

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

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

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

tag: tissue type

value: Breast cancer cell line

tag: sample source

value: Swarbrick Lab (The Garvan Institute)

tag: sample processed

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

tag: sample type

value: Fixed cells

tag: replicate

value: r1, r2:Replicate slide 1/2

tag: technology

value: Xenium

tag: panel size

value: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel (10X Genomics, PN-1000725):5001

tag: panel size custom


title: LG332_218

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in mouse thalamus

library_source: transcriptomic

data_processing:
Gene counts were obtained by aligning reads to human genome (hg38) mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than three cells, cells with a unique gene count over 9000 or less than 300, cells with UMI over 50000 and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
Seurat v3.0.182 R package used for analysis
Assembly: hg38 and mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: thalamus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: thalamus

tag: Sex

value: Female

value: MerTK KO:+/+;PGRN KO:-/-


title: Axl_3

description: mRNA expression in mouse thalamus

value: Male

value: Axl KO:-/-


title: STAMP_114

source_name: PBMC

value: Blood

value: STEMCELL Technologies


title: Starvation, high GFP population, rep 3

description: Library name: Sample 15


title: 19M, mock-infected, day3

description: 10x genomics

value: lung

value: immune cells

value: lung immune cells

value: mock-infected


title: STAMP_101

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)

value: Xenium Prime 5K Human Pan Tissue & Pathways Panel (10X Genomics, PN-1000724):5001


title: 3W, mock-infected, day3

description: 10x genomics


title: Starvation, high GFP population, rep 2

description: Library name: Sample 14

value: human embryonic kidney cells


title: Whole forebrain, 74w old, rep2

first: Paul

last: Frazel

address: 435 E 30th St

institute: NYU Langone Medical Center

data_processing:
After demlutiplexing, cell calling was performed via PIPSeeker software v1.0.0 (PIPseq equivalent of CellRanger)
Assembly: mm10
Supplementary files format and content: Processed data type: count matrix, features, barcodes files. Can be used for tertiary scRNAseq analysis

source_name: Brain

extract_protocol:
Single cell suspensions were generated with papain dissociation, nuclei were generated with dounce homogenization and Sigma EZ buffer.
PIPseq manufcaturer's instructions (Illumina dual-index library)

value: Brain

value: nuclei

value: 74 weeks-old


title: STAMP_100

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

value: Blood and spiked-in MCF-7 and SK-BR-3 cancer cells

value: STEMCELL Technologies (PBMC), Swarbrick Lab (MCF-7/SK-BR-3, The Garvan Institute)

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

value: Fixed cells

value: Xenium


title: Whole forebrain, 74w old, rep1


title: Starvation, high GFP population, rep 1

description: Library name: Sample 13


title: STAMP_99


title: LG180_1603

description: mRNA expression in mouse thalamus

value: thalamus

value: Male


title: STAMP_98


title: Dentate, Cre virus, rep2

tag: condition

value: Cre virus


title: Starvation, low GFP population, rep 2

description: Library name: Sample 18


title: STAMP_97


title: No treatment, unsorted population, rep 3

description: Library name: Sample 11


title: Dentate, control virus, rep2

value: control virus


title: No treatment, unsorted population, rep 2

description: Library name: Sample 10


title: STAMP_96


title: No treatment, unsorted population, rep 1

description: Library name: Sample 9


title: Dentate, Cre virus, rep1


title: STAMP_95

source_name: PBMC, MCF-7

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

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

value: Xenium Human Immuno-oncology Panel (10X Genomics, PN-1000654):380


title: No treatment, low GFP population, rep 4

description: Library name: Sample 8


title: STAMP_94


title: No treatment, low GFP population, rep 3

description: Library name: Sample 7


title: E13-FL-260820-H8

city: Freiburg

first: Nina

last: Peltokangas

address: Stübeweg 51

country: Germany

data_processing:
Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 or 2.20.0.422
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Assembly: ENCODE VM9
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Fetal liver

growth_protocol: Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

extract_protocol:
Endothelial and hematopoietic cells were isolated from E8.5-E9.5 yolk sac, E9.5-E11.5 AGM, E11.5-E13.5 placenta and E12.5-E14.5 fetal liver. For AGM we used the method described by (Boisset et al., 2010), in which the head and the tail of the embryo are cut and a buffer containing antibodies (CD31, Kit) is injected into the aorta allowing the simultaneous removal of blood and staining of the inner wall of the aorta. After staining, the AGM was dissected from the trunk. The corresponding tissues were pooled together for further processing. For single-cell suspension, yolk sac was digested with TrypLE for 5-10 min at 37˚C, while AGM and minced placenta were digested in 1.2 mg/ml collagenase I at 37˚C for 1-1.5h. Fetal livers were either grinded or digested with 1.2 mg/ml or 3 mg/ml collagenase I for 5-10 min at 37˚C. The samples were then filtered (YS, placenta = 40 µm; AGM = 35 µm; fetal liver = 30, 40 and 70 µm). Contaminating red blood cells were removed from the single-cell suspension of placenta and fetal liver samples by density gradient centrifugation (Ficoll).
As described in CEL-Seq2 protocol (Hashimshony et al. 2016) and its modified version (Herman et al., 2018).
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: No treatment was performed

value: Fetal liver

value: Lin-Kit+

tag: developmental stage


title: Dentate, control virus, rep1

value: Brain


title: E13-FL-260820-H7

institute: Max Planck Institute of Immunobiology and Epigenetics


title: STAMP_93

value: Blood

value: STEMCELL Technologies


title: E13-FL-260820-H9


title: No treatment, unsorted population, rep 4

description: Library name: Sample 12

value: human embryonic kidney cells


title: No treatment, low GFP population, rep 2

description: Library name: Sample 6


title: No treatment, low GFP population, rep 1

description: Library name: Sample 5


title: No treatment, high GFP population, rep 4

description: Library name: Sample 4


title: E13-FL-260820-H5


title: No treatment, high GFP population, rep 3

description: Library name: Sample 3


title: Mesothelioma_TMA1_[Xenium_multi_modal]

city: Houston

first: Ken

last: Chen

state: TX

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

description: Xenium multimodal

hyb_protocol: Padlock probes, designed to hybridize to specific target RNA sequences, are added to the tissue.

scan_protocol: The Xenium Analyzer performs on-instrument imaging and decoding of the amplified probes. Nuclei are stained with DAPI for visualization and cell segmentation for Xenium unimodal assay. The Xenium Multi-Tissue Stain Mix provides four types of labeling: antibody staining for membranes, antibody staining for cell interiors, a universal interior label (18S rRNA), and DAPI for nuclear staining fo Xenium multi-modal assay.

data_processing: Xenium ranger pipeline was performed to generate processed data files.

label: Xenium Human Probe Set

source_name: Mesothelioma

label_protocol: Xenium Human Probe Set

growth_protocol: No growth protocol

extract_protocol: No extraction protocol

treatment_protocol: No treatment protocol

value: pleural mesothelioma


title: Mesothelioma_TMA2_[Xenium_unimodal]

description: Xenium unimodal


title: E13-FL-260820-H4


title: E13-FL-260820-H3


title: No treatment, high GFP population, rep 2

description: Library name: Sample 2


title: Mesothelioma_TMA1_[Xenium_unimodal]

description: Xenium unimodal


title: Lung_Adenocarcinoma_TMA2_[Xenium_multi_modal]

description: Xenium multimodal

source_name: Lung Adenocarcinoma

value: lung adenocarcinoma


title: No treatment, high GFP population, rep 1

description: Library name: Sample 1


title: Lung_Adenocarcinoma_TMA2_[Xenium_unimodal]

description: Xenium unimodal


title: MSC EV let7b

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

description:
Library name: Sample 6
Short-read sequencer Illumina NextSeq 200. Column in mirbase_readcounts.csv and featurecounts_readcounts.csv: MSC_EV_let7b

data_processing:
miRNA-Seq reads were first trimmed using CutAdapt v4.0.  Unique molecular identifiers (UMIs) were then extracted from trimmed reads and appended to read named using UMI-tools extract (v1.1.5).
Reads were aligned to human miRNA sequences from miRbase using Bowtie2 v2.4.4. miRbase sequences were padded by 5 base pairs at both ends with native hg38 (GRCh38.97) sequences to maximize alignment rates.
Mapped reads were filtered with Samtools v1.15.1 such that matches were required to be between sixteen and twenty-eight base pairs in length, with no gaps, less than one mismatches, and a MAPQ score ≥ 20.  Remaining reads were deduplicated based on UMI sequences with UMI-tools dedup (--method unique). Reads aligning to miRbase were counted using Samtools-idxstats to estimate expression levels.
To facilitate detection of RNAs absent in miRbase, unmapped reads were aligned to the hg38 genome using Bowtie2 in very-sensitive-local mode, dedpulicated, and filtered following the same criteria above, and assigned to genes using featureCounts (Subread v2.0.1).
Assembly: hg38 (GRCh38.97)
Supplementary files format and content: csv file containing raw counts aligned to miRBase
Supplementary files format and content: csv file containing raw counts aligned to hg38 genome

source_name: Bone marrow

growth_protocol: Human bone Marrow-Derived MSCs were obtained from the ATCC (Cat # PCS-500-012). MSCs were cultured according to the manufacturer’s instructions using the ATCC media (2% FBS: up to passage 4).

extract_protocol:
RNA was isolated from 10µL of either control MSC EVs (no transfection), negative control miRNA transfected MSC EVs (NC MSC EVs) or let-7b-5p transfected MSC EVs (let-7b MSC EVs) using the miRNeasy Kit (Qiagen, Germantown, MD, Catalog #217004). In some cases RNA concentrations were too low to quantify, thus, the entire volume of extracted RNA was desiccated to 5ul.
Qiaseq smRNA library preparation kit (Qiagen) was used for all samples and the workflow was performed according to manufacturer’s instructions, using 24 cycles for final library PCR.

treatment_protocol: MSCs were transfected with a miRNA mimic negative control (NC, that has no known targets in mice or P. aeruginosa) or miRNA let-7b-5p, obtained from Ambion (Austin TX) using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, Waltham, MA). One flask of MSCs was not transfected at all, referred to as control or untreated (UT)  MSCs. The media were harvested one day after the transfection. EVs were purified from the MSC culture supernatants using the ExoQuick-TC EV isolation kit (#EXOTC50A-1, Systems Biosciences Palo Alto, CA).

value: Bone marrow

value: mesenchymal stromal cells extracellular vesicles


title: E13-FL-260820-H2


title: E13-FL-260820-H1


title: RNA_H1_siFAM189A2_R1

city: Durham

first: Tongyu

last: Sun

state: NC

address: 307 research drive

institute: Duke university

description: Library name: RNAseq33

library_source: genomic

data_processing:
Raw reads were trimmed using Fastp (0.20.0) and aligned to the hg38 genome using HISAT2 (2.1.0) with default settings. Reads on each gene were counted using featureCounts (2.0.1). Differentially expressed genes were determined using DESeq2 (1.36.0).
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: H1 hESCs

growth_protocol: Human pluripotent stem cells are maintained in the mTseR plus medium(Stemcell Tech, 100-0276) according to manufacturer's instructions and detached using EDTA/PBS or accutase.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research, 11-331) according to manufacturer's instructions, treated with DNase to remove genomic DNA,
RNA-seq libraries were generated using the Total RNA with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB, 7770S) following the manufacturer's instructions

value: H1 hESCs


title: Mesothelioma_TMA2_[Xenium_multi_modal]

description: Xenium multimodal


title: E13-FL-260820-H6


title: E13-FL-260820-H15


title: MSC EV UT

description:
Library name: Sample 4
Short-read sequencer Illumina NextSeq 200. Column in mirbase_readcounts.csv and featurecounts_readcounts.csv: MSC_EV_UT


title: E13-FL-260820-H14


title: RNA_H1_siCTRL_R2

description: Library name: RNAseq32


title: RNA_H1_siCTRL_R1

description: Library name: RNAseq31


title: MSC NC

description:
Library name: Sample 2
Short-read sequencer Illumina NextSeq 200. Column in mirbase_readcounts.csv and featurecounts_readcounts.csv: MSC_NC

value: mesenchymal stromal cells


title: MSC let7b

description:
Library name: Sample 3
Short-read sequencer Illumina NextSeq 200. Column in mirbase_readcounts.csv and featurecounts_readcounts.csv: MSC_let7b


title: MSC UT

description:
Library name: Sample 1
Short-read sequencer Illumina NextSeq 200. Column in mirbase_readcounts.csv and featurecounts_readcounts.csv: MSC_UT


title: RNA_mesoderm_siFAM189A2_R1

description: Library name: RNAseq29

source_name: mesoderm

value: mesoderm


title: E13-FL-260820-H13


title: Human_Multiome_ATAC

city: Chicago

first: Noah

last: Gamble

state: IL

department: Pathology

institute: University of Chicago

data_processing:
Following sequencing, BCL files were converted to FASTQ using cellranger-arc (v2.0.2) mkfastq. FASTQ files were aligned to the mm10 or hg38 genome assembly using cellranger-arc count. ATAC fragment files were used as inputs to the ArchR (v1.0.2) analysis pipeline in R (v4.3.2). Transcript count matrices were used as inputs to the Seurat gene expression analysis pipeline.
Assembly: mm10 or hg38
Supplementary files format and content: BAM
Supplementary files format and content: Zip file of multiome processed results
Library strategy: scMultiome

source_name: Thymus

extract_protocol:
Mouse: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  Human: Excised thymic tissue from one patient (3-month-old male) was obtained during the course of corrective cardiac surgery at the Advocate Children’s Hospital, Chicago, IL, USA. Patient was de-identified upon receipt with written informed consent for release of genomic sequence data in accordance with IRB approved protocols by the Advocate Children’s Hospital, University of Chicago, and the National Institute of Health. Connective tissue was removed, and stromal tissue was minced using scissors. Tissue was incubated with rotation in DMEM-F12 (Sigma) at 4C for 20min to liberate thymocytes. Further thymocyte liberation was achieved via enzymatic digestion using 0.5mg/mL Collagenase D (Millipore 11088858001) and 0.2mg/mL DNase I (Sigma 10104159001) at 37C for 20min. Remaining fragments were incubated with rotation in 0.5mg/mL Papain (Worthington), 0.25mg/mL Collagenase D and 0.1mg/mL DNase I at 37C for 20min. Digestion was quenched by addition of FACS buffer. Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 (BioLegend 324245 clone 9C4 1:100) and EpCAM+ cells were enriched via positive selection with magnetic anti-Cy7 beads (Miltenyi). Enriched fraction was stained with DAPI (Invitrogen), CD45 (BioLegend 368508 clone 2D1 1:100), LY51/CD249 (Fisher Scientific BDB564533 clone 2D3/APA 1:100) and HLA-DRA (BioLegend 307622 clone L243 1:100) and sorted on a Symphony S6 (BD Biosciences).
For all multiome experiments, we used the ATAC+GEX single-cell kit and protocol (10X Genomics 1000236 with protocol CG000338 RevE) with minor modifications to sample preparation. Briefly, 40,000 mTECs were FACS-sorted into 1X PBS supplemented with 2% BSA and centrifuged at 300rcf for 5 min. Cells were gently washed in 50uL Lysis Buffer (10mM Tris, 10mM NaCl, 3mM MgCl2 in nuclease-free water) and centrifuged at 300rcf for 5 min. Cells were resuspended in  50uL permeabilization buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, 0.01% digitonin, and RNase inhibitor (Millipore) in nuclease-free water) and incubated for 5 minutes on ice. Nuclei were gently washed with wash buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, and RNase inhibitor in nuclease-free water) and centrifuged at 500rcf for 5 min. Finally, nuclei wee resuspended in 5uL chilled diluted nuclei buffer (10X Genomics) and added to transposition mix. Paired-end, dual-index sequencing was performed on the Illumina NextSeq 500 or NovaSeq 6000 platform.

value: Thymus

value: mTEC


title: E13-FL-260820-H12


title: E13-FL-260820-H10


title: RNA_mesoderm_WT_R2

description: Library name: RNAseq28


title: E13-FL-260820-H11


title: RNA_mesoderm_WT_R1

description: Library name: RNAseq27


title: Human_Multiome_GEX


title: RNA_H1_siFAM189A2_R2

description: Library name: RNAseq34


title: E13-FL-020920-H9


title: MSC EV NC

description:
Library name: Sample 5
Short-read sequencer Illumina NextSeq 200. Column in mirbase_readcounts.csv and featurecounts_readcounts.csv: MSC_EV_NC


title: RNA_DE_YAPKO_R2

description: Library name: RNAseq26

source_name: definitive endoderm

value: definitive endoderm


title: E13-FL-260820-H16


title: HCT116 cells, SMC5-DOX-1

city: Jinan

first: Xiaoxia

last: Gong

state: Shandong

address: No. 6699 Qingdao, Huaiyin District

institute: Shandong First Medical University

data_processing:
Run the Liunx gunzip command to decompress the data package
Assembly: The sequencing data is compared to the reference genome by the command tophat
Supplementary files format and content: Assemble transcripts by the command cufflinks

growth_protocol: HCT116 cells are grown in DMEM medium with 10% fetal bovine serum (FBS)  and 1% penicillin mixed with streptomycin (PS), and the cells were grown at 37 °C in a humidified atmosphere of 5% CO2 and 95% air

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher, Waltham, MA, USA) according to the manufacturer`s instructions. Lastly, the concentration, quality and integrity of the total RNA were determined using a Nano Drop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manfacturer's protocols

treatment_protocol: cells were treated with 1000 nM doxorubicin for 24 hours. PBS without drug served as a negative control.

value: Human colorectal cancer cell line

value: SMC5 overexpression

tag: treatment

value: 1000 nM doxorubicin treatemnt for 24 hours


title: E13-FL-020920-H7

value: Fetal liver

value: Lin-Kit+


title: RNA_YAP_WT_R2

description: Library name: RNAseq24

tag: cell line


title: HCT116 cells, SMC5-2

tag: cell type

value: PBS


title: RNA_DE_YAPKO_R1

description: Library name: RNAseq25


title: RNA_YAP_WT_R1

description: Library name: RNAseq23


title: HCT116 cells, SMC5-1


title: E13-FL-020920-H8

tag: tissue


title: RNA_mesoderm_siFAM189A2_R2

description: Library name: RNAseq30


title: HCT116 cells, NSE4-DOX-2

tag: genotype

value: NSE4 overexpression


title: E13-FL-020920-H5


title: aging_study_Age_50_Surv_80_Rep1

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Library name: aging_study_Age_50_Surv_80_Rep1

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing. Post deplexing, FASTQ files were quality inspected using the FastQC tool (available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the MultiQC tool (Ewels et al., 2016). For reference mapping (BDGP6), the nf-core RNA-Seq Seq pipeline was used (version 3.10.1; available at https://nf-co.re/rnaseq) in conjunction with select parameters (--outFilterMultimapNmax 500, --winAnchorMultimapNmax 500, --clip_r1 10, --clip_r2 10). To enumerate counts for known genes, the featureCounts tool was used (Liao et al., 2014). To enumerate counts for transposable elements (TEs), the TEcount tool was used (Jin et al., 2015). Enumerated counts across known genes and TEs were then row concatted by sample and saved as tab-delimited text files.
Assembly: BDGP6
Supplementary files format and content: Tab-delimited text files describing expression in counts for known genes and TEs.

organism: Drosophila melanogaster

source_name: Whole Fly

growth_protocol: All experiments were performed on wild type adult male Drosophila melanogaster (Oregon R; y+ w+). Flies were maintained on Nutri-Fly Bloomington formulation food (Genesee Scientific, Raleigh/Durham NC) at 25°C and 50% humidity on a 12:12 hour light:dark cycle. For aging of flies, males and females were collected within 24 hours of eclosion by anesthetization with CO2 and transferred to fresh vials. After three days, males and females were separated on a CO2 pad and males only were placed into fresh vials, with 20 flies per vial. Any flies that died before separation of males and females were not included in either the aging or supine study. Aging male flies were flipped to fresh vials twice weekly, each time counting the number of dead and censored flies, until the population mortality reached ~20%. A fly was censored if it escaped, if it was stuck to the vial, if it was stuck to the food but still moving, or if it was removed for downstream analyses.   For the aging study, 3 flies (each from a separate vial) were gently removed each day without anaesthesia, using a mouth pipette once the population mortality reached ~20% (~day 50). Removed flies were frozen immediately in liquid nitrogen and stored at -80C for later RNA isolation. Daily removal of flies continued until the population mortality reached ~80 – 85 % (~day 70). After that, remaining flies were allowed to age until the entire population was dead. Additionally, when the population mortality reached ~50%, an additional 20 flies were collected, frozen in liquid nitrogen, and stored at -80C for later RNA isolation. The % mortality associated with the chronological age of each fly on its day of collection was interpolated from the survival curve of the entire population.  For the supine study, flies were checked three times daily for supine behavior once the population mortality reached ~20%. Supine behavior was defined as a fly remaining on its back for more than 10 seconds but still moving. Supine flies were gently removed from the vial using a mouth pipette. Half of these flies were immediately frozen in liquid nitrogen and stored at -80C for later RNA isolation. The other half of these flies were gently placed into a fresh vial for continued observation every few hours during the day, until they died. Note that there was a period of ~14 hours each night where no observations were made. Removal of supine flies continued daily until the population mortality reached ~80%, after which the remaining flies in the population were allowed to age until the entire population was dead. The % mortality associated with the chronological age of each fly on its day of collection was interpolated from the survival curve of the entire population.

extract_protocol:
Individual flies were homogenized in Lysis Binding Mix (from MagMAX mirVana Total RNA Isolation Kit; Thermo Fisher Scientific, Washington, DC; #A27828) using Navy Eppendorf RNA Lysis Kits (Next Advance, Troy, NY; #NAVYE5-RNA) and a Bullet Blender Storm 24 (Next Advance, Troy, NY; #4116-BBY24M). RNA was then isolated from these homogenates using the MagMAX mirVana Total RNA Isolation Kit as described in the manufacturer’s instructions, in conjunction with the KingFisher Apex Purification System with 96 Deep-Well head (Thermo Fisher Scientific, Washington, DC; #5400930).
RNA quality and quantity was first assessed by NanoDrop (Thermo Fisher Scientific, Washington, DC) and High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA). cDNA libraries were generated from 500 ng of total RNAusing NEBNext Ultra II Directional Poly-A RNA Library Prep Kit for Illumina (New EnglandBiolabs, Ipswich, MA; #E7760). cDNA library quality and quantity were assessed byTapeStation 2200 and Qubit (Thermo Fisher Scientific, Washington, DC). cDNA librarieswere sequenced on a NextSeq 2000 machine using NextSeq 2000 P3 reagents (Illumina,San Diego, CA).

value: Whole Fly

tag: strain

value: Oregon R; y+ w+

tag: study

value: aging

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

value: Male

tag: supine death_phenotype


title: HCT116 cells, NSE4-DOX-1


title: RNA_DE_soft_R2

description: Library name: RNAseq22


title: E13-FL-020920-H6


title: HCT116 cells, NSE4-1


title: HCT116 cells, NSE4-2


title: E13-FL-020920-H2


title: E13-FL-020920-H3


title: E13-FL-020920-H4


title: HCT116 cells, GFP-DOX-2

value: WT


title: RNA_DE_soft_R1

description: Library name: RNAseq21


title: E13-FL-020920-H1


title: HCT116 cells, GFP-DOX-1


title: RNA_DE_siFAM189A2_R2

description: Library name: RNAseq18


title: HCT116 cells, SMC5-DOX-2


title: RNA_DE_stiff_R1

description: Library name: RNAseq19


title: Tunicamycin treatment, high GFP population, rep 1

description: Library name: Sample 37

value: human embryonic kidney cells


title: RNA_DE_stiff_R2

description: Library name: RNAseq20


title: HCT116 cells, GFP-2


title: E13-FL-020920-H16


title: RNA_DE_siFAM189A2_R1

description: Library name: RNAseq17


title: HCT116 cells, GFP-1


title: RNA_DE_WT_R2

description: Library name: RNAseq16


title: iPS-epi_Torin103

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: iPSC derived epicardial cell

growth_protocol: hiPSC-EPI was differentiated from hiPSC line 409B2 by modulating WNT and BMP4 signaling and maintained with TGFb inhibitor. Mouse embryonic epicardial cell was emerged from heart explant ex vivo and maintained with TGFb inhibitor. MEC1 was maintained without TGFb inhibitor.

extract_protocol:
RNeasy Micro Kit
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: Cells were treated with Rapamycin (200 nM), Tacrolimus (200 nM) or Torin1 (200 nM) for 7 days before extraction.

value: iPSC derived epicardial cell


title: E13-FL-020920-H15


title: E13-FL-020920-H14


title: RNA_DE_WT_R1

description: Library name: RNAseq15


title: E13-FL-020920-H13


title: RNA_H1_FAM_LTR7_deletion_RNA_R4

description: Library name: RNAseq14

value: H1 hESCs


title: iPS-epi_Torin102


title: Tobacco leaf tissue - WT4_rep2

city: Guiyang

first: Jiajun

last: Luo

state: Guizhou

address: Guizhou University, Guiyang, Guizhou Province

institute: GUIZHOU university

description: Tobacco variety NC82

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Supplementary files format and content: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 15 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.

organism: Nicotiana tabacum

source_name: Young Leaf

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq   sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 ×   150bp read length)

value: seedling stage

value: Young Leaf

value: wildtype

tag: variety

value: Treatment at 4 degree C for 24 hours


title: RNA_H1_FAM_LTR7_deletion_RNA_R3

description: Library name: RNAseq13


title: iPS-epi_Torin101


title: RNA_H1_WT_R4

description: Library name: RNAseq12


title: E13-FL-020920-H11


title: E13-FL-020920-H10


title: Tobacco leaf tissue - OE4_rep1

description: Overexpression of NtPhyA gene

value: Overexpression of NtPhyA gene


title: Tobacco leaf tissue - WT4_rep3

description: Tobacco variety NC82


title: iPS-epi_control03

value: control


title: Tobacco leaf tissue - OE4_rep2

description: Overexpression of NtPhyA gene


title: RNA_H1_soft_RNA_R2

data_processing:
Raw reads were trimmed using Fastp (0.20.0) and aligned to the hg38 genome using HISAT2 (2.1.0)with default settings. Reads on each gene were counted using featureCounts (2.0.1). Differentially expressed genes were determined using DESeq2 (1.36.0).
Assembly: hg38
Supplementary files format and content: bigwig


title: iPS-epi_control02


title: iPS-epi_control01


title: RNA_H1_WT_R3

description: Library name: RNAseq11


title: Tobacco leaf tissue - WT4_rep1

description: Tobacco variety NC82


title: Tobacco leaf tissue - OE4_rep3

description: Overexpression of NtPhyA gene


title: RNA_H1_soft_RNA_R1


title: Sham IP, rep4

city: Changsha

first: Xinran

last: Hou

state: Hunan

address: Xiangya Road 87

institute: Central South University

data_processing:
Low quality bases were trimmed by Trimmomatic (version: 0.38) with  parameters as “ILLUMINACLIP:MeRIP-PE.fa:2:30:10:1:true SLIDINGWINDOW:30:15 AVGQUAL:15 LEADING:15 TRAILING:15 HEADCROP:8 MINLEN:30”.
Clean reads were mapped to Mus musculus genome (GRCm39) using hisat2 (version: 2.1.0) with default parameters.
The alignment file (SAM) was transformed to BAM file and was filtered by the following steps: (1) only keep unique properly aligned reads; (2) remove reads with low MAPQ (< 30). (3) remove reads mapped to black list regions.
The R package exomePeak (version: 2.1.2) was used to call peaks and detect differential peaks from filtered alignment files with parameters as“WINDOW_WIDTH = 200 SLIDING_STEP = 30 FRAGMENT_LENGTH = 200 DIFF_PEAK_ABS_FOLD_CHANGE = 1.5 FOLD_ENRICHMENT = 1.5”.
Assembly: GRCm39
Supplementary files format and content: Annotation and quantification of peaks in known genes

source_name: spinal cord

extract_protocol:
The lumbar enlargement spinal cord was quickly isolated out, removed the meninges, snap frozen in liquid nitrogen, and cryopreserved at -80 ℃. Total RNA was extracted by Trizol reagent (Invitrogen, USA), followed by measuring the concentration by Qubit Fluorometer (Thermo Fisher Scientific, USA) and evaluating the integrity by agarose gel electrophoresis and an Agilent 2100 Bioanalyzer (Agilent, USA).
The MeRIP libraries were constructed using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech, USA) according to the manufacturer’s protocol. Briefly, the eluted immunoprecipitated m6A RNA and input RNA without immunoprecipitation were directly conducted first-strand cDNA synthesis, the addition of Illumina adapters and indexes, purification of the RNA-Seq library, and depletion of ribosomal cDNA. Libraries for IP RNA were PCR amplified for less than 16 cycles and input libraries were less than 12 cycles. All libraries were analyzed by an Agilent 2100 Bioanalyzer (Agilent, USA) and quantified by real-time PCR.

treatment_protocol: Approximately (1-3) ×10^5 living or heat-killed Lewis lung carcinoma cells were implanted into lef femoral cavity

tag: fraction

value: IP

value: spinal cord

value: sham-operated

value: 21 days after tumor inoculation


title: RNA_H1_stiff_RNA_R2


title: Sham IP, rep3


title: Sham IP, rep2


title: Mesothelioma_TMA1_[CosMx]

description: CosMx

hyb_protocol: RNA ISH probes were denatured and hybridized overnight at 37°C. After hybridization, samples were washed and incubated with antibody cocktails and DAPI.

scan_protocol: The prepared samples were loaded onto the SMI instrument for scanning. Reporter probes were hybridized and imaged over multiple cycles to capture RNA and protein signals.

data_processing: CosMx SMI pipeline was performed to generate expMat, metadata, FOV positions, polygon and tx files.

label: barcoded probes

label_protocol: Fluorophore-conjugated antibodies and DAPI were used for staining, targeting proteins such as PanCK, CD45 and CD3.

value: pleural mesothelioma


title: Sham IP, rep1


title: Mesothelioma_TMA2_[CosMx]

description: CosMx


title: 2_iPS-epi_Torin101


title: RNA_H1_stiff_RNA_R1


title: 2_iPS-epi_Torin102


title: E13-FL-020920-H12

value: Fetal liver

value: Lin-Kit+


title: 2_iPS-epi_Tacrolimus

value: Tacrolimus


title: Lung_Adenocarcinoma_TMA2_[CosMx]

description: CosMx

value: lung adenocarcinoma


title: RNA_H1_TEAD1-KO_RNA_R2


title: Sham Input, rep4

value: Input


title: Lung_Adenocarcinoma_TMA1_[CosMx]

description: CosMx


title: 2_iPS-epi_Rapamycin02

value: iPSC derived epicardial cell

value: Rapamycin


title: Sham Input, rep3


title: T79-NEG_CONTROL_SI-2

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: Library name: T79-NEG_CONTROL_SI-2

data_processing:
The reads were mapped with STAR 2.7.11a to the human genome (hg38). The counts for each gene were obtained using quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default.
Assembly: hg38
Supplementary files format and content: Gene expression matrix

source_name: aortic vascular smooth muscle cell

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen) and the RNase-free DNase Set. RNA integrity was assessed using the Agilent Tapestation and samples with RIN >9 were used for sequencing
Libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced on the Illumina NovaSeqX to ~30 million depth with 50 bp paired-end reads.

value: PRIMARY

value: aortic vascular smooth muscle cell

value: Negative Control 1 - siRNA


title: RNA_H1_TEAD1-KO_RNA_R1

value: H1 hESCs


title: Sham Input, rep2


title: RNA_H1_YAP-KO_RNA_R2


title: 2_iPS-epi_control02

value: control


title: T79-NEG_CONTROL_SI-1

description: Library name: T79-NEG_CONTROL_SI-1


title: T79-MCAM-1SI-2

description: Library name: T79-MCAM-1SI-2

value: MCAM siRNA


title: 2_iPS-epi_control01


title: BCP IP, rep4

value: IP

value: spinal cord

value: bone cancer pain


title: T79-MCAM-1SI-1

description: Library name: T79-MCAM-1SI-1


title: RNA_H1_WT_RNA_R2


title: BCP IP, rep3

value: 21 days after tumor inoculation


title: BCP IP, rep2


title: ChIP_H1_WT_RAD21_R1

data_processing:
ChIP-seq reads were trimmed using fastp (0.20.0) using default settings.
ChIP-seq reads were aligned to the hg38 genome using Bowtie version 2.4.4. Only uniquely mapping reads without mismatches were retained.
To create ChIP-seq coverage plots, bam files were converted to bigwig files using bamCoverage and renormalized using RPKM.
Peaks were called uing MACS2 v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells were crosslinked using 1% formaldehyde in the medium at room temperature for 10 min and the cross-linking reactions were quenched using glycine. Chromatin solutions were prepared by adding 1mL of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris, pH 8.1) to the pellets and sonicated using Covaris M220.
For H3K9me3 and H3K27ac ChIP, 20 μg of chromatin was incubated with 5 μg antibody and Dynabeads (Life Technologies, 11204D) overnight at 4 °C. After the incubation, the beads were collected and washed by Low Salt Immune Complex Wash Buffer( 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), High Salt Immune Complex Wash Buffer( 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris, pH 8.1) and TE buffer.

value: WT


title: R88-vSMC-2

description: Library name: R88-vSMC-2

value: Non-transfected


title: ChIP_H1_WT_TEAD1_R2


title: R88-vSMC-1

description: Library name: R88-vSMC-1


title: BCP Input, rep4


title: 2_iPS-epi_Rapamycin01


title: BCP Input, rep3


title: Sham Input, rep1

value: sham-operated


title: R88-NEG_CONTROL_SI-1

description: Library name: R88-NEG_CONTROL_SI-1


title: ChIP_H1_TEAD1-KO_H3K27ac_R2

tag: antibody


title: RNA_H1_YAP-KO_RNA_R1


title: R88-MCAM-1SI-2

description: Library name: R88-MCAM-1SI-2


title: BCP Input, rep2


title: ChIP_H1_TEAD1-KO_H3K27ac_R1


title: BCP Input, rep1


title: ChIP_H1_YAP-KO_H3K27ac_R2

value: YAP-KO


title: RNA_H1_WT_RNA_R1


title: R88-NEG_CONTROL_SI-2

description: Library name: R88-NEG_CONTROL_SI-2


title: NSCs DEK cOE 3

city: Hangzhou

first: sunli

last: cai

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

growth_protocol: primary neural stem cells were isolated from the SVZ of adult C57BL/6 mice brain and maintained in Neuralbasal medium supplemented with 2% B27 in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
primary SVZ tissue were micro-dissected from adult C57BL/6 mice brain and dissociated by Neural Tissue Dissociation Kit - Papain (Miltenyi, 130-092-628)
RNA libraries were pereared for sequencing using standrard lllumina protocols

treatment_protocol: DEK conditional overexpression was induced by treatment of 24 hour neural stem cells infected with AAV9-GFAP-DEK-GFP, using AAV9-GFAP-GFP as a control.

value: brain

value: primary cell

value: neural stem cell

value: DEK overexpression


title: ChIP_H1_YAP-KO_H3K27ac_R1


title: PCZ16-NEG_CONTROL_SI-1

description: Library name: PCZ16-NEG_CONTROL_SI-1

value: PRIMARY

value: aortic vascular smooth muscle cell


title: R88-MCAM-1SI-1

description: Library name: R88-MCAM-1SI-1


title: PCZ16-NEG_CONTROL_SI-2

description: Library name: PCZ16-NEG_CONTROL_SI-2

value: Negative Control 1 - siRNA


title: ChIP_H1_WT_TEAD1_R1

value: H1 hESCs


title: BCP IP, rep1


title: NSCs DEK cOE 2


title: Wild Type T96h_replicate G

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

description:
Biological replicate 3 of 3 of timepoint T96h of sexual reproduction time course
2G_T96

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: To facilitate biological materials collecting, S strains from both mating types were grown on cheesecloth (Sefar Nitex 03-48/31 Heiden) or cellophane sheet (cat#1650193, BioRad laboratories, Hercules) previously placed on Petri-dishes containing M2 medium. S mat- strain has been used as male gamete donor and S mat+ as female. the S mat+ strains were grown on M2 Petri-dishes plus cheesecloth.  For each ten points of the time course materials, number of Petri-dishes has been adjusted (5 were used for T-24h, T0h, T6h, T18h, T24h, 4 for T30h, 2 for T42h, 1 for T54h and T96h) to collect 20 to 100 mg of biological. All the time points were grown on cheesecloth except the T-24h (on cellophane sheet). One to five Petri-dishes per time course experiment were thus inoculated simultaneously with a growing S mat- strain and conidia were collected by washing with 1.5 ml of H2O 6 days later. The collected conidia (around 104 microconidies per ml) were pooled and then used to fertilize corresponding number of Petri-dishes of the S mat+ strain which was growing since 4 days. Time just prior the fertilization process was considered as the T0 (0h). The biological material was then collected 6h, 12h, 18h, 24h, 30h, 42h, 54h and 96h hours after fertilization. An additional time point 24h prior fertilization was taken. Three biological replicates issued from three independent time course have been collected for all time points. The RNA pool used as a reference was assembled by combining equal amount of RNA issued from various growth and crosses conditions and has already been described (Bidard et al., BMC research notes, 2010).

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) or cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

value: Wild type S mat +

tag: growth condition

value: harvested after 162h at 28°C and 96 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

tag: mating type

value: mat-

tag: time (post-fertilization)

source_name: Common reference (4 biosources)

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name of biosource 4


title: Wild Type T96h_replicate A

description:
Biological replicate 1 of 3 of timepoint T54h of sexual reproduction time course
2A_T96

tag: strain


title: Wild Type T96h_replicate C

description:
Biological replicate 2 of 3 of timepoint T96h of sexual reproduction time course
2C_T96


title: Wild Type T54h_replicate C

description:
Biological replicate 2 of 3 of timepoint T54h of sexual reproduction time course
2C_T54

value: harvested after 150h at 28°C and 54 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth


title: Wild Type T54h_replicate G

description:
Biological replicate 3 of 3 of timepoint T54h of sexual reproduction time course
2G_T54


title: NSCs DEK cOE 1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ChIP_H1_WT_H3K27ac_R2

value: WT

tag: antibody


title: Wild Type T54h_replicate A

description:
Biological replicate 1 of 3 of timepoint T42h of sexual reproduction time course
2A_T54

tag: growth condition

tag: mating type


title: PCZ16-MCAM-1_SI-1

description: Library name: PCZ16-MCAM-1_SI-1

value: MCAM siRNA


title: Wild Type T42h_replicate C

description:
Biological replicate 2 of 3 of timepoint T42h of sexual reproduction time course
2C_T42

value: harvested after 138h at 28°C and 42 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

tag: time (post-fertilization)

tag: biosource 1


title: Wild Type T42h_replicate G

description:
Biological replicate 3 of 3 of timepoint T42h of sexual reproduction time course
2G_T42

tag: name of biosource 1

tag: biosource 2


title: ChIP_H1_WT_H3K27ac_R1


title: Wild Type T42h_replicate A

description:
Biological replicate 1 of 3 of timepoint T-24h of sexual reproduction time course
2A_T42

tag: name of biosource 2

tag: biosource 3


title: NSCs Control 3

value: brain

value: primary cell

value: neural stem cell


title: LN983-vSMC-2

description: Library name: LN983-vSMC-2

value: PRIMARY

value: aortic vascular smooth muscle cell

value: Non-transfected


title: ChIP_H1_soft_RAD21_R2

value: H1 hESCs

tag: culture condition

value: soft


title: ChIP_H1_soft_RAD21_R1


title: NSCs Control 2


title: Wild Type T30h_replicate G

description:
Biological replicate 3 of 3 of timepoint T30h of sexual reproduction time course
2G_T30

value: Wild type S mat +

value: harvested after 126h at 28°C and 30 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

value: mat-

tag: name of biosource 3

tag: biosource 4

tag: name of biosource 4


title: ChIP_H1_stiff_RAD21_R2

tag: cell line

value: stiff


title: NSCs Control 1

tag: tissue

tag: cell type


title: PCZ16-MCAM-1_SI-2

description: Library name: PCZ16-MCAM-1_SI-2

tag: treatment


title: Wild Type T30h_replicate C

description:
Biological replicate 2 of 3 of timepoint T30h of sexual reproduction time course
2C_T30

tag: strain

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: LN983-NEG_CONTROL_SI-2

description: Library name: LN983-NEG_CONTROL_SI-2

value: Negative Control 1 - siRNA


title: Wild Type T30h_replicate A

description:
Biological replicate 1 of 3 of timepoint T30h of sexual reproduction time course
2A_T30

tag: growth condition


title: Wild Type T24h_replicate G

description:
Biological replicate 3 of 3 of timepoint T24h of sexual reproduction time course
2G_T24

value: harvested after 120h at 28°C and 24 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

tag: mating type


title: Wild Type T24h_replicate C

description:
Biological replicate 2 of 3 of timepoint T24h of sexual reproduction time course
2C_T24

tag: time (post-fertilization)


title: Expression of W80R-Q79K mutant AKT1

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

institute: CNRS/Université Paris Cité

description: TJx9-2_1_S13.resultsRSEM.genes.results "TJx9-2_2_S14.resultsRSEM.genes.results"

data_processing:
a primary analysis based on AOZAN software (version 2.2.1 (revision v2.2.1-0-g4047575), ENS, Paris) was applied to demultiplex and control the quality of the raw data (with bcl2fastq (v2.18.0.12))
Obtained fastq files were then aligned using Bowtie algorithm
Reads count using RSEM (v1.3.1) with the Aligned to Transcriptome bam files
statistical analyses on the read counts were performed with theDESeq2 package version 1.26.0
Assembly: GCF_000001215.4_Release_6_plus_ISO1_MT_genomic
Supplementary files format and content: tab-delimited text files include RSEM values for each Sample (3 replicates/condition)

source_name: ovary

extract_protocol:
Ovaries were dissected in S2 medium (Schneider’s insect medium supplemented with 10% fetal calf serum). Ovaries (30 pairs) were washed three times in calcium-free phosphate buffered saline (PBS) and incubated at 22°C for 30 min with vigorous shaking (2000rpm) in 1 ml of 0.05% trypsin and 5mg/mL collagenase in PBS. Supernatant was removed, filtered through a 30µM nylon mesh into tubes containing 1 ml of S2 medium, pelleted at 1000g for 5 min in a Microcentrifuge, and washed in 1 ml of PBS. For RNAseq experiment, the pellets were resuspend directly in TRI-reagent and store at -80°C. RNA extraction was performed using the TRI-reagent supplier’s instructions (Molecular Research Center, Cincinnati, Ohio, USA).
TruSeq mRNA stranded Illumina

value: ovary

value: follicular cells

tag: genotype

value: TJ-Gal4; W80R-Q79K AKT1


title: ChIP_H1_stiff_RAD21_R1

tag: antibody


title: LN983-NEG_CONTROL_SI-1

description: Library name: LN983-NEG_CONTROL_SI-1

value: PRIMARY

value: aortic vascular smooth muscle cell


title: ChIP_H1_soft_CTCF_R1

value: H1 hESCs

value: CTCF


title: LN983-MCAM-1SI-2

description: Library name: LN983-MCAM-1SI-2

value: MCAM siRNA


title: Expression of T15 mutant AKT1

description: TJx5-2_1_S7.resultsRSEM.genes.results" "TJx5-2_2_S8.resultsRSEM.genes.results" "TJx5-2_3_S9.resultsRSEM.genes.results

value: TJ-Gal4; T15 AKT1


title: LN983-MCAM-1SI-1

description: Library name: LN983-MCAM-1SI-1


title: Expression of T1 mutant AKT1

description: TJx4-2_1_S4.resultsRSEM.genes.results" "TJx4-2_2_S5.resultsRSEM.genes.results" "TJx4-2_3_S6.resultsRSEM.genes.results

value: TJ-Gal4; T1 AKT1


title: LN983-vSMC-1

description: Library name: LN983-vSMC-1

value: Non-transfected


title: G88-vSMC-2

description: Library name: G88-vSMC-2


title: ChIP_H1_stiff_CTCF_R2

value: stiff


title: Wild Type T24h_replicate A

description:
Biological replicate 1 of 3 of timepoint T24h of sexual reproduction time course
2A_T24

value: Wild type S mat +

value: mat-

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: ChIP_H1_stiff_CTCF_R1

tag: culture condition


title: G88-vSMC-1

description: Library name: G88-vSMC-1


title: G88-NEG_CONTROL_SI-2

description: Library name: G88-NEG_CONTROL_SI-2

value: Negative Control 1 - siRNA


title: empty Landing Pad, no AKT1 expression

description: TJx24482_1_S16.resultsRSEM.genes.results" "TJx24482_2_S17.resultsRSEM.genes.results" "TJx24482_3_S18.resultsRSEM.genes.results

value: ovary


title: Expression of AKT1 WT

description: TJx3-2_1_S1.resultsRSEM.genes.results" "TJx3-2_2_S2.resultsRSEM.genes.results" "TJx3-2_3_S3.resultsRSEM.genes.results

value: follicular cells

value: TJ-Gal4; WT AKT1


title: Expression of T5 mutant AKT1

description: TJx6-2_1_S10.resultsRSEM.genes.results" "TJx6-2_2_S11.resultsRSEM.genes.results" "TJx6-2_3_S12.resultsRSEM.genes.results

value: TJ-Gal4; T5 AKT1


title: ChIP_H1_soft_H3K9me3_R1

value: soft


title: SPL_PC_WT_8

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

institute: Universitätsklinikum Erlangen

data_processing:
Removal of low-quality reads and adapter-trimming with TrimGalore (v0.6.6).
Mapping of reads to genome reference with STAR (v2.6.1d)
Quantification of aligned reads with Salmon (v1.4.0) and gene-level summarization
Assembly: GRCm38
Supplementary files format and content: Combined table with summarized gene-wise counts for each sample from Spikevax immunization
Supplementary files format and content: Combined table with summarized gene-wise counts for each sample from non-immunized mice (steady state)

source_name: spleen

growth_protocol: Mice were immunized with mRNA-1273 (Spikevax) subcutaneously on day 0 and boosted day 70. On day 77, bone marrow plasma cells (CD138+ TACI+) were sorted and lysed for total RNA isolation.

extract_protocol:
Plasma cells were FACS-purified (CD138+ TACI+) and sorted directly into beta-mercaptoethanol-containing RLT (Qiagen) Lysis buffer. Total RNA was isolated with the RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Plus kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.

value: spleen

value: plasma cell (CD138+ TACI+)

value: steady state


title: ChIP_H1_soft_CTCF_R2

value: H1 hESCs

value: CTCF


title: Wild Type T18h_replicate A

description:
Biological replicate 1 of 3 of timepoint T18h of sexual reproduction time course
2A_T18

value: harvested after 114h at 28°C and 18 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

tag: name of biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: SPL_PC_WT_6


title: G88-NEG_CONTROL_SI-1

description: Library name: G88-NEG_CONTROL_SI-1

tag: cell line

value: PRIMARY

value: aortic vascular smooth muscle cell


title: SPL_PC_KO_7

tag: tissue


title: Wild Type T18h_replicate C

description:
Biological replicate 2 of 3 of timepoint T18h of sexual reproduction time course
2C_T18

value: Wild type S mat +

value: mat-

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 4

tag: name of biosource 4


title: G88-MCAM-1SI-2

description: Library name: G88-MCAM-1SI-2

tag: cell type

tag: treatment

value: MCAM siRNA


title: G88-MCAM-1SI-1

description: Library name: G88-MCAM-1SI-1


title: ChIP_H1_stiff_H3K9me3_R2

value: stiff


title: Wild Type T12h_replicate G

description:
Biological replicate 3 of 3 of timepoint T12h of sexual reproduction time course
2G_T12

tag: strain

tag: growth condition

value: harvested after 108h at 28°C and 12 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

tag: mating type


title: Wild Type T18h_replicate G

description:
Biological replicate 3 of 3 of timepoint T18h of sexual reproduction time course
2G_T18

tag: time (post-fertilization)


title: Wild Type T12h_replicate A

description:
Biological replicate 1 of 3 of timepoint T12h of sexual reproduction time course
2A_T12

tag: biosource 1


title: Wild Type T12h_replicate C

description:
Biological replicate 2 of 3 of timepoint T12h of sexual reproduction time course
2C_T12

tag: name of biosource 1


title: SPL_PC_KO_5

value: spleen

tag: genotype


title: G82-NEG_CONTROL_SI-1

description: Library name: G82-NEG_CONTROL_SI-1

value: Negative Control 1 - siRNA


title: ChIP_H1_soft_H3K9me3_R2

tag: culture condition

value: soft

tag: antibody


title: SPL_PC_WT_3

value: plasma cell (CD138+ TACI+)

value: steady state


title: Wild Type T6h_replicate G

description:
Biological replicate 3 of 3 of timepoint T6h of sexual reproduction time course
2G_T6

value: harvested after 102h at 28°C and 6 hours after fertilization with microconidia of a wild strain S mat+, M2 media covered with a cheesecloth

tag: biosource 2

tag: name of biosource 2

tag: biosource 3


title: ChIP_H1_stiff_H3K27ac_R1

tag: cell line

value: H1 hESCs


title: ChIP_H1_stiff_H3K9me3_R1


title: Wild Type T6h_replicate C

description:
Biological replicate 2 of 3 of timepoint T6h of sexual reproduction time course
2C_T6

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: G82-NEG_CONTROL_SI-2

description: Library name: G82-NEG_CONTROL_SI-2

value: PRIMARY

tag: cell type

value: aortic vascular smooth muscle cell


title: ChIP_H1_soft_H3K27ac_R2


title: Wild Type T0h_replicate G

description:
Biological replicate 3 of 3 of timepoint T0h of sexual reproduction time course
2G_T0

value: Wild type S mat +

value: harvested after 96h at 28°C, on M2 media covered with cheesecloth, Just prior fertilization

value: mat-

tag: name of biosource 4


title: SPL_PC_KO_4

tag: tissue

tag: treatment


title: ChIP_H1_stiff_H3K27ac_R2


title: G82-MCAM-1SI-2

description: Library name: G82-MCAM-1SI-2

value: MCAM siRNA


title: ChIP_H1_soft_H3K27ac_R1


title: G82-MCAM-1SI-1

description: Library name: G82-MCAM-1SI-1


title: HiCAR_H1-WT_soft_HiCAR_R2

data_processing:
library strategy: HiCAR
The reads were trimmed using cutadapt and mapped to the hg38 genome using BWA-MEM, and then pairs were detected with the pairtools. Only reads with MAPQ>30 were retained. The hic files and mcool files were created with the juicer and the cool tool separately.
Assembly: hg38
Supplementary files format and content: hic

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine at room temperature.
Crosslinked cells were lysed with 400 μL NPB buffer (5% BSA, 1mM DTT, 0.2% IGEPAL, Roche Complete Protease Inhibitor) on ice for 15 min to isolate the nuclei. For tagmentation, the nuclei were resuspended in 50 μL 2X TB buffer (66mM Tris-AC pH 7.8, 132mM KCl-AC, 20mM Mg-AC, 32% DMF), 45 μL molecular biology grade water and 5 μL assembled Tn5 transposase, and rotated at 37°C for 1 h. Then the nuclei were treated by MseI or CviQI for the first digestion, followed by in situ ligation with T4 DNA ligase. The second restriction enzyme digestion was performed using NlaIII, followed by the circularization and PCR amplification.


title: SPL_PC_WT_1


title: Wild Type T6h_replicate A

description:
Biological replicate 1 of 3 of timepoint T6h of sexual reproduction time course
2A_T6

tag: strain

tag: growth condition

tag: mating type

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: BM_PC_WT_8

source_name: bone marrow

value: bone marrow


title: HiCAR_H1-WT_soft_HiCAR_R1


title: MILDd45_REP3

city: Catanzaro

first: Barbara

last: Puccio

address: Viale Europa

department: Dept of Surgical and Medical Sciences

country: Italy

institute: Magna Graecia University of Catanzaro

description:
Library name: Sample 24
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  MILDd45_3

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
After quality control, paired-end clean reads were aligned to the reference genome (Homo Sapiens(GRCh38/hg38)) using Hisat2 v2.0.5.
Assembly: GRCh38/hg38
Supplementary files format and content: xls file includes gene counts for each Sample
Supplementary files format and content: xls file includes fpkm values for each Sample

source_name: induced pluripotent stem cell derived neurons

extract_protocol:
Total RNA was extracted by using TRIzol Reagents (Invitrogen, 15596026), according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.


title: HiCAR_H1-WT_stiff_HiCAR_R2


title: MILDd45_REP2

description:
Library name: Sample 23
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  MILDd45_2

value: induced pluripotent stem cell derived neurons


title: SPL_PC_KO_2

value: spleen


title: BM_PC_KO_7

value: plasma cell (CD138+ TACI+)


title: Wild Type T0h_replicate C

description:
Biological replicate 2 of 3 of timepoint T0h of sexual reproduction time course
2C_T0

tag: time (post-fertilization)

tag: biosource 1

tag: name of biosource 1


title: MILDd15_REP3

description:
Library name: Sample 21
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  MILDd15_3


title: MILDd45_REP1

description:
Library name: Sample 22
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  MILDd45_1


title: BM_PC_WT_6

tag: genotype

value: steady state


title: Wild Type T0h_replicate A

description:
Biological replicate 1 of 3 of timepoint T0h of sexual reproduction time course
2A_T0

tag: biosource 2


title: HiCAR_H1-WT_stiff_HiCAR_R1


title: BM_PC_KO_5


title: HiCAR_YAP-KO_HiCAR_R1


title: HiCAR_YAP-KO_HiCAR_R2


title: Wild Type T-24h_replicate G

description:
Biological replicate 3 of 3 of timepoint T-24h of sexual reproduction time course
2G_T-24

value: harvested after 72h at 28°C, on M2 media covered with cellophane sheet (24 hours before fertilization)

tag: name of biosource 2


title: Basal epithelial cells transfected with stealth SOX9 siRNA (Rep-2)

city: Cincinnati

first: Satish

middle: Kumar

last: Madala

state: Ohio

address: 3235 Eden Ave

department: Internal Medicine

institute: University of Cincinnati

description:
Library name: PP5
18380_SOXsi_2_raw_counts_All_Sample.xlsx

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Assembly: hg19
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

source_name: Lung

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: Primary cells

value: Basal epithelial cells

value: SOX9 siRNA


title: Basal epithelial cells transfected with stealth SOX9 siRNA (Rep-3)

description:
Library name: PP6
18381_SOXsi_3_raw_counts_All_Sample.xlsx


title: MILDd15_REP2

description:
Library name: Sample 20
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  MILDd15_2


title: Basal epithelial cells transfected with stealth SOX9 siRNA (Rep-1)

description:
Library name: PP4
18379_SOXsi_1_raw_counts_All_Sample.xlsx