#This is a list of raw reads directories and a description of their contents. 

#/2018_DP_serum/ #This directory is of 16S V1-V3 reads sequenced by D. Perera at the URI Core from Marcelo Friere serum samples of healthy, type 2 diabetics and T2 diabetics with periodontitis. 
#2023 changed from /2018_Serum/ to /2018_DP_serum/ by M. Ramsey
#2024 moved to *tar.gz and deleted original folder for compression and archiving. 

#/2014_Jorth/ #Changed from /2014_whiteley/ by MR in 2023. This is a collection of RNASeq metatranscriptome reads published in the 2014 jorth mBio paper and used here for alignment to our own RNASeq datasets. 

#/2018_Benitez_Paez/ #changed from /2018_meta/ by MR in 2023. This is a published RNASeq metatranscriptome dataset used identically to the 2014_Jorth dataset. 

#/2018_coculture/

#/2018_DP_serum/

#/2018_subging_gingivitis/

#/2019_hp_oxyr/

#/2020_KapaRNA/

#/2020_Sup_trans/

#/2020_TnSeq/

#/2022_AL_SUPP/

#/2023_AL_SUPP/

#/saliva/ 

#rnaseq_fastq  #relavent fastq files copied and renamed for usage from /2018_coculture/     AL Jul-2023
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x
x

#/2023_EL1_WGS/ # this folder has the raw Ilumina and Nanopore reads for the whole genome sequence of Hp strain EL1 (strain # MR305). Sequene was done by MIGS. The reads were also uploaded on NCBI under the BioProject PRJNA954350 and SRA accession numbers SRR24129362 and SRR25463078. This data was sent for MRA for publication titled: Whole genome sequence of Haemophilus parainfluenzae EL1 isolated from healthy supragingival plaque.     THP Aug-2023

#/2020_TnSeq/ # this folder has all the raw Illumina reads for the TnSeq experiments performed by Thais Palma. See the README document inside the 2020_TnSeq folder that specifies each fastq file.  THP Sep-2023
#/2024_valm/ # this folder is RNASeq reads from Alex Valm for Cmat - A. naeslundii coculture added by MR 5-14-24