This readme.txt file was generated on <20230928> by <Farid Halim>
Recommended citation for the data: 
Abdul Halim, Mohd Farid; Costa, Kyle C.; Fonseca, Dallas; Niehaus, Thomas. (2023). Transcriptomics analysis (RNA-sequencing) of Methanococcus maripaludis wild-type strain and moeA deletion mutant.. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/YY0Q-8870.


-------------------
GENERAL INFORMATION
-------------------

1. Title of Dataset 
Transcriptomics analysis (RNA-sequencing) of Methanococcus maripaludis  wild-type strain and moeA deletion mutant.

2. Author Information

  Principal Investigator Contact Information
        Name:           Kyle Costa
           Institution: University of Minnesota
           Address:     670 Biological Sciences Center
                        1445 Gortner Avenue
                        St. Paul, MN 55108
           Email:       kcosta@umn.edu
	   ORCID:       https://orcid.org/0000-0003-0407-1431

  Associate or Co-investigator Contact Information
        Name:           Mohd Farid Abdul Halim
           Institution: University of Minnesota 
           Address:     685 Biological Sciences Center
                        1445 Gortner Avenue
                        St. Paul, MN 55108
           Email:       faridh@umn.edu
	   ORCID:       https://orcid.org/0000-0002-2327-3621

  Associate or Co-investigator Contact Information
           Name:        Dallas Fonseca
           Institution: University of Minnesota
           Address:     685 Biological Sciences Center
                        1445 Gortner Avenue
                        St. Paul, MN 55108
           Email:       fonse039@umn.edu
           ORCID:

Associate or Co-investigator Contact Information
           Name:        Thomas Niehaus
           Institution: University of Minnesota
           Address:     685 Biological Sciences Center
                        1445 Gortner Avenue
                        St. Paul, MN 55108
           Email:       tniehaus@umn.edu
           ORCID:       https://orcid.org/0000-0002-3575-8001


3. Date of data collection
   20230111 - 20230217

4. Geographic location of data collection (where was data collected?): 
  SeqCenter, 91 43rd St Suite 250, Pittsburgh, PA 15201

5. Information about funding sources that supported the collection of the data:
    U.S. Department of Energy, Office of Science, Basic Energy Sciences under grant number DE-SC0019148

6. Overview of the data (abstract): 
Transcriptomic analysis of total RNA for Methanococcus maripaludis grown in McCas-formate medium. The data compared the RNA abundance between the wild-type strain and the mutant strain with the gene encoding molybdopterin molybdotransferase (moeA, MMP1619) deletion. Released for the submission of manuscript for publication.


--------------------------
SHARING/ACCESS INFORMATION
-------------------------- 

1. Licenses/restrictions placed on the data:
CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/)

2. Links to publications that cite or use the data:
Mohd Farid Abdul Halim, Dallas R Fonseca, Thomas D Niehaus, Kyle C Costa. 2023. Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. bioRxiv 2023.05.09.540023
https://doi.org/10.1101/2023.05.09.540023

3. Was data derived from another source? No
           If yes, list source(s):

4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use


---------------------
DATA & FILE OVERVIEW
---------------------

1. File List
   A. Filename: alignment.tsv       
      Short description: Total RNA reads for all samples submitted.       

   B. Filename: hisat2_counts.tsv       
      Short description: RNA reads count based on the homolog identified.      
        
   C. Filename: 143 Differentially Expressed Genes Heatmap.tiff         
      Short description: 143 Differentially Expressed Genes Heatmap data image 

    D. Filename: 143 Differentially Expressed Genes In DmoeA vs WT.tsv
      Short description: 143 Differentially Expressed Genes list (tsv format)

    E. Filename: 143 Differentially Expressed Genes In DmoeA vs WT.tsv.xlsx
      Short description: 143 Differentially Expressed Genes list (Excel format)

    F. Filename: All Quantified Genes.tsv       
      Short description: All Quantified Expressed Genes list (tsv format)

    G. Filename: All Quantified Genes.tsv.xlsx           
      Short description: All Quantified Expressed Genes list (Excel format)

    H. Filename: Sample PCA.pdf   
      Short description: All sample PCA analysis results

    I. Filename: SeqCenter Project Report 
      Short description: Protocols of experiment by Seqcenter


2. Relationship between files:        
The files contain the raw transcriptomics data of independent samples (biological replicates) of RNA extract from Methanococcus maripaludis wild-type and DmoeA strains.


--------------------------
METHODOLOGICAL INFORMATION
--------------------------

1. Description of methods used for collection/generation of data: 

Five ml of Methanococcus maripaludis wild-type and DmoeA strains were collected by centrifugation. The total RNA were extracted from the cell culture.

2. Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>

Quality control and adapter trimming was performed with bcl-convert [1].  Read mapping was performed with HISAT2 [2].  Read quantification was performed using Subread’s featureCounts [3] functionality.  Mapping statistics can be found in the ‘alignment.tsv’ file.  Raw, quantified counts are available in the “hisat2_counts.tsv” file.  Read counts loaded into R [4] and were normalized using edgeR’s [5] Trimmed Mean of M values (TMM) algorithm.  Subsequent values were then converted to counts per million (cpm).  Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups.  The file “All Quantified Genes.tsv” contains the results of the qlfTest for all genes in addition to the normalized counts per million.  The file “143 Differentially Expressed Genes In DmoeA vs WT.tsv” is a subset of the aforementioned file with |logFC| > 1 and p < .05.  The differentially expressed gene’s normalized counts per million were then used to create a heatmap, “143 Differentially Expressed Genes Heatmap.tiff”.  The PCA, “Sample PCA.pdf” is based on the global expression of all genes in the “All Quantified Genes.tsv” file.  No pathway analysis could be performed for your selected reference.

References:

[1] 	bcl-convert: A proprietary Illumina software for the conversion of bcl files to basecalls.  https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm

[2]	Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).

[3]	Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014

[4]	R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/

[5]	Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140


3. Instrument- or software-specific information needed to interpret the data:
NA

4. Standards and calibration information, if appropriate:
NA

5. Environmental/experimental conditions:
NA

6. Describe any quality-assurance procedures performed on the data:
NA

7. People involved with sample collection, processing, analysis and/or submission:

Mohd Farid Abdul Halim
Dallas Fonseca
SeqCenter RNA Sequencing Services


-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: hisat2_counts.tsv
-----------------------------------------

1. Number of variables: 5


2. Number of cases/rows: 1722


3. Missing data codes:
There is no missing data.

4. Variable List
                  
    A. Name: Locustag
       Description: The gene locus tag identification for Methanococcus maripaludis S2
                   
    B. Name: DmoeA_1
       Description: Raw RNA reads count in the moeA deletion strain - Replicate #1
            
    C. Name: DmoeA_2
       Description: Raw RNA reads count in the moeA deletion strain - Replicate #2
              
    D. Name: WT_1
       Description: Raw RNA reads count in the wild-type strain - Replicate #1

    E. Name: WT_2
       Description: Raw RNA reads count in the wild-type strain - Replicate #2
                    

-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: 143 Differentially Expressed Genes In DmoeA vs WT.tsv
-----------------------------------------

1. Number of variables: 10

2. Number of cases/rows: 143

3. Missing data codes:
There is no missing data. 

4. Variable List
                  
    A. Name: Locustag
       Description: The gene locus tag identification for Methanococcus maripaludis S2

    B. Name: Description
       Description: Annotation of the gene of interest

    C. Name: FeatureType
       Description: Denote gene of interest is based from "Complete DNA sequence (CDS)"
                
    D. Name: logFC
       Description: Log-fold changes of the RNA reads count
                
    E. Name: PValue
       Description: The probability that a particular statistical measure, such as the mean or standard deviation, of an assumed probability distribution will be greater than or equal to (or less than or equal to in some instances) observed results.
               
    F. Name: FDR
       Description: False Discovery Rate
            
    G. Name: WT_1
       Description: Normalized counts per million (cpm) of RNA reads for the wild-type strain - Replicate #1
                   
    H. Name: WT_2
       Description: Normalized counts per million (cpm) of RNA reads for the wild-type strain - Replicate #2
                  
    I. Name: DmoeA_1
       Description: Normalized counts per million (cpm) of RNA reads for the moeA deletion strain - Replicate #1
                   
    J. Name: DmoeA_2
       Description: Normalized counts per million (cpm) of RNA reads for the moeA deletion strain - Replicate #2
                   

-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: All Quantified Genes.tsv
-----------------------------------------

1. Number of variables: 10

2. Number of cases/rows: 1530

3. Missing data codes:
There is no missing data.

4. Variable List
                  
    A. Name: Locustag
       Description: The gene locus tag identification for Methanococcus maripaludis S2
          
    B. Name: Description
       Description: Annotation of the gene of interest
                  
    C. Name: FeatureType
       Description: Denote gene of interest is based from "Complete DNA sequence (CDS)"
                 
    D. Name: logFC
       Description: Log-fold changes of the RNA reads count
                    
    E. Name: PValue
       Description: The probability that a particular statistical measure, such as the mean or standard deviation, of an assumed probability distribution will be greater than or equal to (or less than or equal to in some instances) observed results.
                  
    F. Name: FDR
       Description: False Discovery Rate
                  
    G. Name: WT_1
       Description: Normalized counts per million (cpm) of RNA reads for the wild-type strain - Replicate #1
                    
    H. Name: WT_2
       Description: Normalized counts per million (cpm) of RNA reads for the wild-type strain - Replicate #2
                    
    I. Name: DmoeA_1
       Description: Normalized counts per million (cpm) of RNA reads for the moeA deletion strain - Replicate #1
                   
    J. Name: DmoeA_2
       Description: Normalized counts per million (cpm) of RNA reads for the moeA deletion strain - Replicate #1