README: 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: dequinaa@uci.edu

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 https://doi.org/10.3389/fendo.2023.1279878 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)

https://doi.org/10.3389/fendo.2023.1279878

3. Links to other publicly accessible locations of the data:

https://www.ncbi.nlm.nih.gov/sra/PRJNA1054603

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 (https://doi.org/10.3389/fendo.2023.1279878) can be found at: https://github.com/Leandromvelez/pituitary-LPS-gene-analyses

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

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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.