This neurosphere-transcript-data-readme.txt file was generated on 2021-02-16 by Josi M. Herron GENERAL INFORMATION 1. Title of Dataset: Benzalkonium chloride disinfectants induce apoptosis, inhibit proliferation, and activate the integrated stress response in a 3-D in vitro model of neurodevelopment 2. Author Information A. Principal Investigator Contact Information Name: Libin Xu Institution: University of Washington Address: Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, United States Email: libinxu@uw.edu B. Associate or Co-investigator Contact Information Name: Josi M. Herron Institution: University of Washington Address: Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, United States Email: josiherron01@gmail.com 3. Date of data collection (single date, range, approximate date): 2019-08-14 to 2019-09-16 4. Geographic location of data collection: Seattle, WA 98195, United States 5. Information about funding sources that supported the collection of the data: National Institute of Child Health and Human Development (R01HD092659) National Institute of Environmental Health Sciences (P30ES007033) University of Washington’s Department of Medicinal Chemistry SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: NA 2. Links to publications that cite or use the data: https://pubs.acs.org/doi/full/10.1021/acs.chemrestox.0c00386 3. Links to other publicly accessible locations of the data: NA 4. Links/relationships to ancillary data sets: NA 5. Was data derived from another source? No 6. Recommended citation for this dataset: Herron, Josi M., et al. (2021), Benzalkonium chloride disinfectants induce apoptosis, inhibit proliferation, and activate the integrated stress response in a 3-D in vitro model of neurodevelopment , Dryad, Dataset, https://doi.org/10.5061/dryad.v6wwpzgv5 DATA & FILE OVERVIEW 1. File List: Neurosphere-transcript-data.xlsx This excel workbook contains 3 sheets. The first sheet, titled FPKM, contains 11 columns. Three biological replicates per treatment were used for transcriptomics analyses. Rows contain FPKM values of each transcript, signified by Ensembl IDs and Gene Names. The second and third sheets, titled DEGs_BAC C12 and DEGs_BAC C16, respectively, contain 3 columns. Rows contain the fold change and adjusted P value of each transcript, signified by Gene Names. 2. Relationship between files, if important: NA 3. Additional related data collected that was not included in the current data package: NA 4. Are there multiple versions of the dataset? No METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Total RNA was extracted from each sample and RNA concentration was quantified using a microplate spectrophotometer. RNA integrity was evaluated by formaldehyde agarose gel electrophoresis to visualize the 18S and 28S rRNA bands. RNA integrity and purity were further confirmed by Novogene (Chula Vista, CA) using an Agilent 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, California). Samples with RNA Integrity Number (RIN) of 10.0 or above were submitted for RNA sequencing.  Novogene performed the cDNA library construction and sequencing using the Illumina NovaSeq 6000 platform (150 base pairs paired-end, with sequencing depth above 20 million reads per sample). 2. Methods for processing the data: Raw RNA sequencing reads in FASTQ format were mapped to the mouse genome using HISAT (https://ccb.jhu.edu/software/hisat/index.shtml; Last accessed 8/14/2019) and format conversions were performed using Samtools. Cufflinks (http://cufflinks.cbcb.umd.edu/; Last accessed 8/14/2019) was used to estimate relative abundances of transcripts from each RNA sample. Cuffdiff, a module of Cufflinks, was used to determine differentially expressed genes (DEGs) between control and BAC C12, as well as control and BAC C16. DEGs met the criterion of an adjusted P value < 0.05 (corresponding to the allowed false discovery rate of 5%). 3. Instrument- or software-specific information needed to interpret the data: Microsoft Excel (Version 2007 or later) 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: Neurospheres exposed to BAC C12 (50 nM), BAC C16 (50 nM), or vehicle control from DIV 4 to DIV 5 in 4 wells of a 6-well plate were pelleted. 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Josi M. Herron DATA-SPECIFIC INFORMATION FOR: Neurosphere-transcript-data.xlsx , sheet titled "FPKM" 1. Number of variables: 9 2. Number of cases/rows: 53,562 3. Variable List: gene_short_name - the name of the gene gene_id - the Ensemble Stable identifier of each gene Control 1 - contains FPKM values of transcripts from sample 1 of neurospheres treated with vehicle control Control 2 - contains FPKM values of transcripts from sample 2 of neurospheres treated with vehicle control Control 3 - contains FPKM values of transcripts from sample 3 of neurospheres treated with vehicle control BAC C12 1 - contains FPKM values of transcripts from sample 1 of neurospheres treated with BAC C12 BAC C12 2 - contains FPKM values of transcripts from sample 2 of neurospheres treated with BAC C12 BAC C12 3 - contains FPKM values of transcripts from sample 3 of neurospheres treated with BAC C12 BAC C16 1 - contains FPKM values of transcripts from sample 1 of neurospheres treated with BAC C16 BAC C16 2 - contains FPKM values of transcripts from sample 2 of neurospheres treated with BAC C16 BAC C16 3 - contains FPKM values of transcripts from sample 3 of neurospheres treated with BAC C16 4. Missing data codes: None 5. Specialized formats or other abbreviations used: FPKM (Fragments Per Kilobase of transcript per Million) DATA-SPECIFIC INFORMATION FOR: Neurosphere-transcript-data.xlsx , sheet titled "DEGs_BAC C12" 1. Number of variables: 3 2. Number of cases/rows: 117 3. Variable List: symbol - a unique abbreviation for the gene name logfc - log fold change of the transcript abundance from neurospheres treated with BAC C12 relative to abundance of same transcript from neurospheres treated with vehicle control adjpv - adjusted p-value 4. Missing data codes: None 5. Specialized formats or other abbreviations used: DEGs (Differentially expressed genes), logfc (log fold change), adjpv (adjusted p value) DATA-SPECIFIC INFORMATION FOR: Neurosphere-transcript-data.xlsx , sheet titled "DEGS_BAC C16" 1. Number of variables: 3 2. Number of cases/rows: 38 3. Variable List: symbol - a unique abbreviation for the gene name logfc - log fold change of the transcript abundance from neurospheres treated with BAC C16 relative to abundance of same transcript from neurospheres treated with vehicle control adjpv - adjusted p-value 4. Missing data codes: None 5. Specialized formats or other abbreviations used: DEGs (Differentially expressed genes), logfc (log fold change), adjpv (adjusted p value)