We analyzed the field of expression profiling by high throughput sequencing, or HT-seq, in terms of replicability and reproducibility, using data from the NCBI GEO (Gene Expression Omnibus) repository.

Archived dataset contains following files:

- output/parsed_suppfiles.csv, p-value histograms, histogram classes, estimated number of true null hypotheses (pi0).

- output/document_summaries.csv, document summaries of NCBI GEO series

- output/publications.csv, publication info of NCBI GEO series

- output/scopus_citedbycount.csv, Scopus citation info of NCBI GEO series

- output/single-cell.csv, single cell experiments

- spots.csv, NCBI SRA sequencing run metadata

- suppfilenames.txt, list of all supplementary file names of NCBI GEO submissions. One filename per row.

- suppfilenames_filtered.txt, list of supplementary file names used for downloading files from NCBI GEO. One filename per row.

Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided to help users query and download experiments and curated gene expression profiles.

Modern humans spend most of their time having eaten recently. The purpose of the current project is to understand how the blood, which contains immune cells, responds in the hours after eating a meal that is moderately high in fat. We used a sequencing method to observe the expression of all the genes in blood cells in five participants who were each fed a high fat meal on three separate days. The results are reported in the manuscript, “Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal." Overall design: We used a sequencing method to observe the expression of all the genes in blood cells in five participants who were each fed a high fat meal on three separate days, resulting in 45 whole blood transcriptomes. For each sample, 3 mL of venous whole blood was drawn into a Tempus Blood RNA tube, shaken vigorously, and then frozen at -80°C until use. Total RNA was purified with the Tempus Spin RNA Isolation Kit with minor modifications to the manufacturer’s protocol. To remove residual genomic DNA, RNA samples were treated on-column with RNase-Free DNase per manufacturer’s instructions. RNA quantity, quality, and integrity were assessed with NanoDrop 1000 and 2100 Bioanalyzer. All isolated RNA had A260/A280 ratios greater than 2 and RNA integrity numbers higher than 7.3. RNA-Seq libraries were constructed at the DNA Technologies and Expression Core at the University of California, Davis, using the Ovation Human Blood RNA-Seq Library System (NuGEN Technologies). Sequencing was performed in a 2x100bp format with 45 samples multiplexed on 3 lanes on an Illumina HiSeq 4000. Analysis of the data is reported in the manuscript, “Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal.”

This template is for recording genome data from the NimbleGen platform. This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

GEO (Gene Expression Omnibus) is a public functional genomics data repository supporting MIAME-compliant data submissions. There are also tools provided to help users query and download experiments and curated gene expression profiles.

Table of Contents

Main Description File Descriptions Linked Files Installation and Instructions

1. Main Description

This is the Zenodo repository for the manuscript titled "A TCR β chain-directed antibody-fusion molecule that activates and expands subsets of T cells and promotes antitumor activity.". The code included in the file titled marengo_code_for_paper_jan_2023.R was used to generate the figures from the single-cell RNA sequencing data. The following libraries are required for script execution:

Seurat scReportoire ggplot2 stringr dplyr ggridges ggrepel ComplexHeatmap

File Descriptions

The code can be downloaded and opened in RStudios. The "marengo_code_for_paper_jan_2023.R" contains all the code needed to reproduce the figues in the paper The "Marengo_newID_March242023.rds" file is available at the following address: https://zenodo.org/badge/DOI/10.5281/zenodo.7566113.svg (Zenodo DOI: 10.5281/zenodo.7566113). The "all_res_deg_for_heat_updated_march2023.txt" file contains the unfiltered results from DGE anlaysis, also used to create the heatmap with DGE and volcano plots. The "genes_for_heatmap_fig5F.xlsx" contains the genes included in the heatmap in figure 5F.

Linked Files

This repository contains code for the analysis of single cell RNA-seq dataset. The dataset contains raw FASTQ files, as well as, the aligned files that were deposited in GEO. The "Rdata" or "Rds" file was deposited in Zenodo. Provided below are descriptions of the linked datasets:

Gene Expression Omnibus (GEO) ID: GSE223311(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223311)

Title: Gene expression profile at single cell level of CD4+ and CD8+ tumor infiltrating lymphocytes (TIL) originating from the EMT6 tumor model from mSTAR1302 treatment. Description: This submission contains the "matrix.mtx", "barcodes.tsv", and "genes.tsv" files for each replicate and condition, corresponding to the aligned files for single cell sequencing data. Submission type: Private. In order to gain access to the repository, you must use a reviewer token (https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html).

Sequence read archive (SRA) repository ID: SRX19088718 and SRX19088719

Title: Gene expression profile at single cell level of CD4+ and CD8+ tumor infiltrating lymphocytes (TIL) originating from the EMT6 tumor model from mSTAR1302 treatment. Description: This submission contains the raw sequencing or .fastq.gz files, which are tab delimited text files. Submission type: Private. In order to gain access to the repository, you must use a reviewer token (https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html).

Zenodo DOI: 10.5281/zenodo.7566113(https://zenodo.org/record/7566113#.ZCcmvC2cbrJ)

Title: A TCR β chain-directed antibody-fusion molecule that activates and expands subsets of T cells and promotes antitumor activity. Description: This submission contains the "Rdata" or ".Rds" file, which is an R object file. This is a necessary file to use the code. Submission type: Restricted Acess. In order to gain access to the repository, you must contact the author.

Installation and Instructions

The code included in this submission requires several essential packages, as listed above. Please follow these instructions for installation:

Ensure you have R version 4.1.2 or higher for compatibility.

Although it is not essential, you can use R-Studios (Version 2022.12.0+353 (2022.12.0+353)) for accessing and executing the code.

1. Download the *"Rdata" or ".Rds" file from Zenodo (https://zenodo.org/record/7566113#.ZCcmvC2cbrJ) (Zenodo DOI: 10.5281/zenodo.7566113).
2. Open R-Studios (https://www.rstudio.com/tags/rstudio-ide/) or a similar integrated development environment (IDE) for R.
3. Set your working directory to where the following files are located:

marengo_code_for_paper_jan_2023.R Install_Packages.R Marengo_newID_March242023.rds genes_for_heatmap_fig5F.xlsx all_res_deg_for_heat_updated_march2023.txt

You can use the following code to set the working directory in R:

setwd(directory)

1. Open the file titled "Install_Packages.R" and execute it in R IDE. This script will attempt to install all the necessary pacakges, and its dependencies in order to set up an environment where the code in "marengo_code_for_paper_jan_2023.R" can be executed.
2. Once the "Install_Packages.R" script has been successfully executed, re-start R-Studios or your IDE of choice.
3. Open the file "marengo_code_for_paper_jan_2023.R" file in R-studios or your IDE of choice.
4. Execute commands in the file titled "marengo_code_for_paper_jan_2023.R" in R-Studios or your IDE of choice to generate the plots.

This is the GitHub repository for the single cell RNA sequencing data analysis for the human manuscript. The following essential libraries are required for script execution: Seurat scReportoire ggplot2 dplyr ggridges ggrepel ComplexHeatmap Linked File: -------------------------------------- This repository contains code for the analysis of single cell RNA-seq dataset. The dataset contains raw FASTQ files, as well as, the aligned files that were deposited in GEO. Provided below are descriptions of the linked datasets: 1. Gene Expression Omnibus (GEO) ID: GSE229626 - Title: Gene expression profile at single cell level of human T cells stimulated via antibodies against the T Cell Receptor (TCR) - Description: This submission contains the matrix.mtx, barcodes.tsv, and genes.tsv files for each replicate and condition, corresponding to the aligned files for single cell sequencing data. - Submission type: Private. In order to gain access to the repository, you must use a "reviewer token"(https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html). 2. Sequence read archive (SRA) repository - Title: Gene expression profile at single cell level of human T cells stimulated via antibodies against the T Cell Receptor (TCR) - Description: This submission contains the "raw sequencing" or .fastq.gz files, which are tab delimited text files. - Submission type: Private. In order to gain access to the repository, you must use a "reviewer token" (https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html). Please note that since the GSE submission is private, the raw data deposited at SRA may not be accessible until the embargo on GSE229626 has been lifted. Installation and Instructions -------------------------------------- The code included in this submission requires several essential packages, as listed above. Please follow these instructions for installation: > Ensure you have R version 4.1.2 or higher for compatibility. > Although it is not essential, you can use R-Studios (Version 2022.12.0+353 (2022.12.0+353)) for accessing and executing the code. The following code can be used to set working directory in R: > setwd(directory) Steps: 1. Download the "Human_code_April2023.R" and "Install_Packages.R" R scripts, and the processed data from GSE229626. 2. Open "R-Studios"(https://www.rstudio.com/tags/rstudio-ide/) or a similar integrated development environment (IDE) for R. 3. Set your working directory to where the following files are located: - Human_code_April2023.R - Install_Packages.R 4. Open the file titled Install_Packages.R and execute it in R IDE. This script will attempt to install all the necessary pacakges, and its dependencies. 5. Open the Human_code_April2023.R R script and execute commands as necessary.

To understand the diversity of expression states in IDH-wildtype Glioblastomas, we profiled 24,131 single cells from 28 patients with GBM by single-cell RNA sequencing (7,930 cells by Smartseq2 and 16,201 by 10X). Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2 (main text) or 10X (supplementary text).--------------------------------------------------------------Authors state "We have difficulties in approving raw data submission to GEO or dbGAP and are therefore submitting at this point only the processed data and the metadata (both attached) and will continue in parallel with the process of granting approval for raw data submission in dbGAP and another repository (DUOS). "

Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to identify small RNAs (sRNAs) from both barley and Bgh that regulate gene expression both within species and cross-kingdom. Overall design: 90 samples analyzed = 5 genotypes * 6 time points * 3 replications Note: This experiment used the identical split-plot design, tissue, and source RNA as GEO submission # 101304 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101304).

PFHxS, PFOS, and Heptachlor RNA sequencing data. Portions of this dataset are inaccessible because: The files are too large. They can be accessed through the following means: The data can be accessed through the hyperlinks. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190490 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190009. Format: Raw RNA-sequencing output files (fastq files) for PFOS exposure located https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190490. Metadata is included with the GEO submission. Raw RNA-sequencing output files (fastq files) for PFHxS exposure located https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190009. Metadata is included with the GEO submission. This dataset is associated with the following publication: Gutsfeld, S., L. Wehmas, I. Omoyeni, N. Schweiger, D. Leuthold, P. Michaelis, X.M. Howey, S. Gaballah, N. Herold, C. Vogs, C. Wood, L. Becker-Bertotto, G. Wu, N. Kluver, W. Busch, S. Scholz, J. Schor, and T. Tal. Investigation of Peroxisome Proliferator-Activated Receptor Genes as Requirements for Visual Startle Response Hyperactivity in Larval Zebrafish Exposed to Structurally Similar Per- and Polyfluoroalkyl Substances (PFAS). ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 132(7): 77007, (2024).

We analyzed the field of expression profiling by high throughput sequencing, or RNA-seq, in terms of replicability and reproducibility, using data from the NCBI GEO (Gene Expression Omnibus) repository. Our work puts an upper bound of 56% to field-wide reproducibility, based on the types of files submitted to GEO.

Archived dataset contains following files:

- output/parsed_suppfiles.csv, p-value histograms, histogram classes, estimated number of true null hypotheses (pi0).

- output/document_summaries.csv, document summaries of GEO series

- output/publications.csv, publication info of GEO series

- output/scopus_citedbycount.csv, Scopus citation info of GEO series

- output/single-cell.csv, single cell experiments

- spots.csv, sequencing run metadata: number of spots and bases

- suppfilenames.txt, list of all supplementary file names of GEO submissions. One filename per row.

- suppfilenames_filtered.txt, list of supplementary file names used for downloading files from NCBI GEO. One filename per row.

Several studies have suggested a relationship between SARS-CoV-2 infection and diabetes. This study examined the consequences of infection of human pancreatic islets with SARS-CoV-2 virus. This GEO submission contains the raw and processed data from single-cell RNA sequencing (scRNAseq) experiments evaluating the tropism of SARS-CoV-2 in pancreatic islets and transcriptional changes induced by infection of these cells. Overall we observed limited infection of pancreatic islets (0.2 - 3.4% of all cells infected per donor) and identified multiple pancreatic cell types as targets of infection; due to the preponderance of major endocrine cell populations in our islet cell preparations, downstream analyses were primarily focused on alpha and beta cells. Within beta cells we identified an upregulation of interferon stimulated genes in both infected and bystander cells as well as an NFκB mediated genes in infected cells only. Within alpha cells we detected a non-specific downregulation of a large number of host genes in infected cells. Pancreatic islets from three donors were infected or mock infected with SARS-CoV-2 for 48 hours then analyzed by scRNAseq.

The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros, a critical regulator of lymphopoiesis and leukemogenesis. Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice. Of particular relevance, fingers 1 and 4 contributed to distinct stages of B- and T-cell development and finger 4 was selectively required for tumor suppression in thymocytes and in a new model of BCR-ABL+ acute lymphoblastic leukemia. These results, combined with transcriptome profiling (this GEO submission: RNA-Seg of whole thymus from wt and the two ZnF mutants), reveal that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions, and they demonstrate that selective mutagenesis can facilitate efforts to elucidate the functions and mechanisms of action of this prevalent class of factors. Overall design: RNA-Seq from Whole Thymus comparing wt (3 replicates), Ikaros-ZnF1-/- mutant (2 replicates) and Ikaros-ZnF4-/- mutant (2 replicates) RPKM_Thymocytes.txt (linked below as a supplementary file) reports the relative mRNA expression levels (RPKM)values for all annotated Refseq genes that had at least one read in at least one of the samples, with duplicates for the same gene (different transcripts for same gene) filtered out. RPKM (Mortazavi et al., 2008) were calculated based on exonic reads obtained by using the software SeqMonk (Babraham Bioinformatics) and reference genome annotations from NCBI (mm9).

Clinical information with SRA and GEO submission numbers

Array Manufacturer: Illumina Inc., Distribution: commercial, Technology: oligonucleotide beads, The HumanHT-12 v4 Expression BeadChip provides high throughput processing of 12 samples per BeadChip without the need for expensive, specialized automation. The BeadChip is designed to support flexible usage across a wide-spectrum of experiments. The updated content on the HumanHT-12 v4 Expression BeadChips provides more biologically meaningful results through genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants. Each array on the HumanHT-12 v4 Expression BeadChip targets more than 31,000 annotated genes with more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data. These should be submitted as part of a GEOarchive. Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html

Array Manufacturer: Illumina, Inc., Distribution: custom-commercial, Technology: oligonucleotide beads, The HumanRef-8 v3.0 Expression BeadChip features up-to-date content derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database (Build 36.2, Release 22). Please use the GEO Data Submission Report Plug-in v1.0 for Gene Expression which may be downloaded from https://icom.illumina.com/icom/software.ilmn?id=234 to format the normalized and raw data. These should be submitted as part of a GEOarchive. Instructions for assembling a GEOarchive may be found at http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html

Administration of public lands includes controlling rights of access, surface rights and subsurface rights, or mineral rights. Public lands are administered for all Albertans through the issuance of dispositions. A disposition must be obtained for any access to or activity on public lands. Applicants for a disposition must submit the appropriate plan type that meets the requirements for the activity and purpose of the disposition being applied for. Disposition plans submitted digitally, and digital plan submissions are to be appropriately geo-referenced.

Uploaded datasets are detailed exposure information (chemical concentrations and water quality parameters) for exposures conducted in a flow through diluter system with larval Pimephales promelas to four different pyrethroid pesticides. The GEO submission URL links to the NCBI GEO database and contains gene expression data from whole larvae exposed to different concentrations of the pyrethroids across multiple experiments. This dataset is associated with the following publication: Biales, A., M. Kostich, A. Batt, M. See, R. Flick, D. Gordon, J. Lazorchak, and D. Bencic. Initial Development of a Multigene Omics-Based Exposure Biomarker for Pyrethroid Pesticides. CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY. CRC Press LLC, Boca Raton, FL, USA, 179(0): 27-35, (2016).

Table S1. Detailed representation of data obtained from GEO. ARDS gene expression submissions were retrieved from GEO using two terms “Acute lung injury” and “Lung injury”, which resulted in 23 and 25 data sets, respectively. These 48 entries were filtered down to 31 entries according to conditions described in Methods. The reason for filtering out an experiment is provided. (XLSX 16 kb)

Data from: Cell-type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development

https://doi.org/10.5061/dryad.3bk3j9kxv

Description of the data and file structure

These files contain the raw Western blot and immunohistochemistry (IHC) image data used for figure generation and CHD8 quantification in the embryonic wild type and Chd8+/- mouse cortex, as described in Yim et al. Cell Genomics 2025.

For the IHC data, raw ZVI image files and exported image files of the merged and individual channels are included, organized by time point: E12.5, E14.5, E16.0, and E17.5. Image file names include the litter ID (C#-#), embryo ID (P#), slide number (S#), and image ID information. For images of individual channels, file names include the immunostained protein or nuclear stain in that channel (e.g., _CHD8, _Hoechst).

Files and their structure

Western_blots.tar.gz

Description: West...