DOI: 10.5061/dryad.x69p8czrd
title: Bulk RNAseq of chronic LPS treated female mouse pituitary across doses

description: To investigate the mechanisms of chronic inflammation on gonadotropin
 secretion we performed bulk RNA-seq on pituitaries from female mice
 chronically exposed to lipopolysaccharide for 6 weeks.
description: Pituitaries were dissected between 10 to 11 am from
 mice after 6 weeks of twice weekly i.p. injections and when they reache
 diestrous. The pituitaries were frozen in RNAlater (Qiagen) at minus 80
 degrees Celsius. RNA was
 harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was
 used for the construction of sequencing libraries. 
 RNA libraries for RNA-seq were prepared using SMARTER
 mRNA-Seq Library Prep Kit following manufacturer's
 protocols. RNA-seq
 CLC Genomics Workbench v
 11.0.1 Sequence reads were
 trimmed for adaptor sequence/low-quality sequence using CLC genomic
 benchwork (parameter- Quality limit: 0.05) 
 Trimmed sequence reads were mapped to GrCM38/mm10
 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3
 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
 Read count extraction and normalization
 were performed using CLC genomic benchwork
description: # GENERAL INFORMATION 1\. Title of Dataset: Bulk RNAseq of chronic LPS
 treated female mouse pituitary across doses 2\. Author Information
                 Principal Investigator Contact Information               
  Name: Dequina Nicholas                             Institution:
 University of California Irvine                 Address: Irvine, CA USA  
               Email: 3\. Date of data collection
 (single date, range, approximate date): 2019-2022 4\. Geographic location
 of data collection: La Jolla, CA and Irvine, CA 5\. Experimental summary
 of dataset contents, contextualized in experimental procedures and
 results: This dataset provides the raw and normalized counts for bulk RNA
 sequencing performed on pituitaries derived from LPS treated female mice.
 Four mice per group were treated with increasing doses of LPS by
 twice-weekly intraperitoneal injections for 6 weeks. The total mRNA from
 pituitaries from mice in diestrus was extracted. After creation of
 ribodepleted libraries, the samples were sequenced. Analysis of this
 dataset is published at 
 and demonstrated substantial remodeling of the pituitary transcriptome in
 response to chronic LPS treatment. 6\. Information about funding sources
 that supported the collection of the data: NIH NICHD K99 HD098330 and R00
 HD098330 ## **SHARING/ACCESS INFORMATION** 1\. Licenses/restrictions
 placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2\. Links to
 publications that cite or use the data: Garcia C, Velez LM, Ujagar N, Del
 Mundo Z, Nguyen T, Fox C, Mark A, Fisch KM, Lawson MA, Duleba AJ, Seldin
 MM. and Nicholas DA. Lipopolysaccharide-induced Chronic Inflammation
 Increases Female Serum Gonadotropins and Shifts the Pituitary
 Transcriptomic Landscape. Front. Endocrinology (2023)
 3\. Links to other
 publicly accessible locations of the data:
 4\.
 Links/relationships to ancillary data sets: None 5\. Was data derived from
 another source? No 6\. Code used for analysis in the associated
 publication () can be
 found at:
 7\.
 Recommended citation for this dataset: Garcia C, Velez LM, Ujagar N, Del
 Mundo Z, Nguyen T, Fox C, Mark A, Fisch KM, Lawson MA, Duleba AJ, Seldin
 MM. and Nicholas DA. Lipopolysaccharide-induced Chronic Inflammation
 Increases Female Serum Gonadotropins and Shifts the Pituitary
 Transcriptomic Landscape. Front. Endocrinology (2023) ## **DATA & FILE
 OVERVIEW** 1\. File List: A) normed_cpms_filtered_annot.csv B)
 raw_annotated_combined.counts 2\. Relationship between files, if
 important: normed_cpms_annot.csv are normalized RNA counts derived from
 the data file raw_annotated_combined.counts 3\. Additional related data
 collected that was not included in the current data package: None 4\. Are
 there multiple versions of the dataset? No                A. If yes, name
 of file(s) that was updated: NA                               i. Why was
 the file updated? NA                               ii. When was the file
 updated? NA
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: normed_cpms_filtered_annot.csv 1\. Number
 of Samples: 16 2\. Number of treatment groups: 4 3\. Treatment
 abbreviations and definitions: * PBS: Samples 01 to 04 are PBS control
 mice injected with phosphate buffered saline equivalent to the volume used
 to inject LPS in the experimental groups twice weekly for weeks. * Lo:
 Samples 05 to 08 are mice injected with LPS (5ng/kg) twice weekly for 6
 weeks. * Med: Samples 09 to 12 are mice injected with LPS (500ng/kg) twice
 weekly for 6 weeks. * Hi: Samples 13 to 16 are mice injected with LPS
 (50ug/kg) twice weekly for 6 weeks. 4\. Sample List: PBS_01 PBS_02 PBS_03
 PBS_04 Lo_05    Lo_06    Lo_07    Lo_08    Med_09             
 Med_10              Med_11              Med_12              Hi_13   
 Hi_14    Hi_15    Hi_16\ 5\. Number of genes/rows: 451 6\. Column labels
 A) id: Column A has the Ensembl gene ID for the gene in that row. B)
 SYMBOL: Column B has the gene symbols for the gene in that row. C)
 gene_type: Column C has the gene type for the gene in that row. D-F)
 Headers are the sample identifiers. The letters represent dose, and the
 numbers represent the biological replicate. Data in these columns
 normalized counts per million mapped reads. DATA-SPECIFIC INFORMATION FOR:
 raw_annotated_combined.counts 1\. Number of Samples: 16 2\. Number of
 treatment groups: 4 3\. Treatment abbreviations and definitions: * PBS:
 Samples 01 to 04 are PBS control mice injected with phosphate buffered
 saline equivalent to the volume used to inject LPS in the experimental
 groups twice weekly for weeks. * Lo: Samples 05 to 08 are mice injected
 with LPS (5ng/kg) twice weekly for 6 weeks. * Med: Samples 09 to 12 are
 mice injected with LPS (500ng/kg) twice weekly for 6 weeks. * Hi: Samples
 13 to 16 are mice injected with LPS (50ug/kg) twice weekly for 6 weeks.
 4\. Sample List: PBS_02_S50_L004           Lo_06_S54_L004            
 Med_10_S58_L004         Hi_15_S63_L004             
 Hi_14_S62_L004              Med_09_S57_L004        
 Lo_07_S55_L004             Lo_08_S56_L004            
 PBS_01_S49_L004           Hi_13_S61_L004             
 Lo_05_S53_L004             PBS_04_S52_L004          
 PBS_03_S51_L004           Hi_16_S64_L004             
 Med_12_S60_L004         Med_11_S59_L004\ 5\. Number of genes/rows: 2768
 6\. Column labels A) id: Column A has no label and has the Ensembl gene ID
 for the gene in that row. B-Q) Headers are the sample identifiers. The
 letters represent dose, and the numbers represent the biological
 replicate. Data in these columns are raw counts combined from pair end
 reads per sample for each gene. SXX_L004 are identifiers from the
 sequencing run. R) SYMBOL: Column B has the gene symbols for the gene in
 that row.