FASTQ files are named as follows:

Assay_Collab_FixedRNAcellpool#_TypeOfSample_Batch_OrderOfProcessing_GEMwell_PoolForSeq_S*_L***_R*_001.fastq.gz

Assay = what type of sequencing is this (here - Fixed RNAseq seq ("Flex") by 10X genomics)
Collab = Collaboration with Paz Lab for TBI project in this case; all files should note this
FixedRNAcellpool# = Designates pool of nuclei prior to probe hybridization in Fixed RNAseq workflow
TypeOfSample = cell type; ex - Brain nuclei 
Batch = Processing batch; considered same batch if loaded onto GEM same day
OrderOfProcessing = if library preps done on different days with different reagents, these are considered separate batches
GEMwell = if samples were pooled on GEM wells or not on that specific chip
PoolForSeq = pooled libraries to be sequenced as the same submission or not. 

And _S*_L***_R*_001.fastq.gz is autogenerated by the core and corresponds to the Illumina naming convention:
S* = The sample number based on the order that samples were listed in the sample sheet.
L*** = The lane number
R* = The read number
001.fastq.gz = standard Illumina file ending for FASTQ files