=================================
Human Controls
=================================

At least 1 control strip was used per amplification set (96 well plate), containing 2 wells without cells (termed ERCC), 2 wells without cells or ERCC (termed NTC), 10pg Human Universal Reference (Takara 636538) and 2 wells of 10 pg Control RNA provided in the Takara kit.  Takara control RNA is a mouse RNA control, so it is aligned and included in the mouse control data set.  

For more details, please see the Documentation tab in the Cell Types web application.

Gene expression data matrices
	human-aligned_controls_2018-10-04_exon-matrix.csv
		Contains the (row, column) matrix of read counts obtained for each (gene, sample) based on alignment to exons.
		The first row contains the unique identifiers of the samples (controls)
		The first column contains the unique identifiers of the genes
	human-aligned_controls_2018-10-04_intron-matrix.csv
		Contains the (row, column) matrix of read counts obtained for each (gene, sample) based on alignment to introns.
		The first row contains the unique identifiers of the samples (controls)
		The first column contains the unique identifiers of the genes

Sample information (human-aligned_controls_2018-10-04_samples-columns.csv)
	seq_name
		unique identifier for sequencing
	sample_id
		Numeric cell id
	sample_type
		Nuclei, Cell or Control
	organism
		Donor species
	donor_id
		Unique donor mouse identifier
	sex
		Sex of donor mouse. F, female; M, male
	age_days
		Age of donor in days (for Human data age was give in years and multiplied by 365)
	brain_hemisphere
		Brain hemisphere of disected cells
	brain_region
		Brain region targeted for sampling
	brain_subregion
		Brain subregion targeted for sampling	
	facs_date
		The date on which cells were collected by FACS. All dissections were performed on the same date as the FACS date for each sample.
	facs_container
		FACS container unique identifier
	sample_name
		FACS well id identifying sample
	facs_sort_criteria	
		Gating criteria used to select cells for sorting
	rna_amplification_set
		Amplificaiton plate
	library_prep_set
		Library plate
	library_prep_avg_size_bp
		Average bp size of Library (Fragment Analyzer™ Automated CE)
	seq_name
		unique identifier for sequencing
    	seq_tube
		Sequencing Lane
	seq_batch
		Sequencing Batch (with date)
	total_reads
		Total number of sequencing reads
	percent_exon_reads
		% unique genomic reads aligned to exons (STAR)
	percent_intron_reads
		% unique genomic reads aligned to introns (STAR)
	percent_intergenic_reads
		% unique genomic reads aligned to intergenic sequence (STAR)
	percent_rrna_reads
		% total reads aligned to rRNA (STAR)
	percent_unique_reads
		% total reads aligned to genome and unique (STAR)
	percent_synth_reads
		% total reads aligned to ERCC synthetic mRNA (STAR)      
	percent_ecoli_reads
		% total reads aligned to E. coli (STAR)
	percent_aligned_reads_total
		% total reads aligned (STAR)
	complexity_cg
		Dinucleotide odds ratio (PRINSEQ)
	genes_detected_cpm_criterion
		# of genes with CPM values greater than 0, intron and exon counts included
	genes_detected_fpkm_criterion
		# of genes with FPKM values greater than 0, only exon counts included

Gene information (human-aligned_controls_2018-10-04_genes-rows.csv)
	gene
		Gene symbol
	chromosome
		Chromosome location of gene
	entrez_id
		NCBI Entrez ID
	gene_name
		Gene name
	mouse_homologenes
		Mouse ortholog