Listed below are the various repositories for data as well as resources for troubleshooting.
NCBI
The National Center for Biotechnology Information Contains a variety of different databases and tools, including GEO and SRA below, as well as Pubmed and BLAST.
GEO
Gene Expression Omnibus Originally for microarrays, now for other expression data sets as well. Repository for data retention and reproducibility.
SRA
Short Reads Archive For anything that isnt uploaded into GEO, there are other repositories available but SRA is the general repository for any short reads data. The better the metadata as well, the better the data can be further mined in the future.
EBI
European Bioinformatics Institute The European equivalent of NCBI. They additionally have a variety of databases and tools, major ones being the ENA and Ensembl.
ENA
European Nucleotide Archive Equivalent to the SRA- provides a repository for nucleotide storage.
Ensembl
Ensembl A genome exploration tool and repository. Similar to general NCBI genome databases, contains annotations for genomes as well as the base reference genomes for a variety of organisms.
StackOverflow
StackOverflow Forum site for code troubleshooting. A great place to search for solutions to different code problems, or post a question you may have. ALWAYS SEARCH BEFORE POSTING Odds are pretty high that your question or an iteration of it have been already asked.
BioStars
BioStars Similar to StackOverflow, but specifically for bioinformatics. Both are incredible tools.