#Inventory of this directory are for RNASeq analyses. 

/EA21_analysis/
|empty file folders, once was CM SC rnaseq #jul-2023 AL


/2018-EA_subging_gingivitis/ #jul-2023 AL, need to confirm that the actual data, done by EA #RNaseq analysis for CM vs CM in subgingval gingavitis


/EA21_aligment/ #various aligments for CM in different environments, done by EA #jul-2023 AL

|RNAseq for CM in mono cultures vs s.sal 
|CM mono vs whitely meta data
|2020_kapa 


/2021__KLemon/

/transcriptome_analyses/ #previous master files for RNAseq analyses, done by EA and DP from 2020-2021 #jul-2023 AL 

|hp_sm_aerobic
|oxry
|hpara_sm_anaerobic
|2014whioteley_vs_hp
|hp_anero_vs_aero
|aerobic_w_peroxide 


/2020_transcriptome_analyses_AL/ #folder containing RNAseq analysis by AL in 2020

|smhp_ana_vs_espinoza
|sm_mono_aero_vs_ana
|fastq

/2023_MM_RNAseq/ #folder containing RNAseq analysis by MM in 2023
 
/2023_AL_RNAseq/ #folder containing RNAseq analysis by AL in 2023
|script testing
  		 - testing environement for scripts in making
|2023_SM_AL
  		- RnaSeq of S. mitis (aero/ana) in cocultures
|2023_HP_AL
  		- Rnaseq of H. para (areo/ana) in coculures
|2023_CM_AL
  		-Rnaseq of C. mat (areo/ana) in coculures
|2023_SM_aero_vs_Benitez_Meta
  		- SM mono aero against BP 2014 metatranscriptome
|2023_SM_aero_vs_Jorth_Meta_2014
  		- SM mono aero against Jorth 2014 metatranscriptome

|2024_avalm 
	- Cmat vs A. naeslundii, data from Alex Valm by MR 5-14-24, 2 types of experiment, one with both live, one with Cmat only, Anaes heat killed.

|2025_jasmer_hp
	- Hpara typestrain in coculture with A253 salivary gland cells from Dr. Kim Jasmer at ULSD. This is Hp monoculture vs a253 coculture.

|2026_jasmer_hp
	- Identical experiments to 2025_jasmer_hp but for Hp with OKF6 epithelial cells instead of A253 to suss out differences between Hp responses to the two different human cell types.
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