Single Cell Analysis Program - Transcriptome (SCAP-T) (UCSD)

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Demographics (1)

SURGERY_YEAR - Year of surgery (phv00222022.v6.p1)

Other (122)

3polyA(first) - Number of first reads trimmed for polyA from 3' end (phv00222112.v6.p1)
3polyA(second) - Number of second reads trimmed for polyA from 3' end (phv00222113.v6.p1)
5polyT(first) - Number of first reads trimmed for polyT from 5' end (phv00222110.v6.p1)
5polyT(second) - Number of second reads trimmed for polyT from 5' end (phv00222111.v6.p1)
ADDITIONAL_SAMPLE_COMMENTS - Additional sample comments (phv00222067.v6.p1)
AmbiguousMappedExonic - Number of reads that mapped ambiguosly to exons of more than one gene and were not counted (phv00222128.v6.p1)
AmbiguousMappedIntronic - Number of reads that mapped ambiguosly to introns of more than one gene and were not counted (phv00222281.v7.p1)
ANALYTE_TYPE - Analyte type (phv00222015.v6.p1)
aRNAPrimer(first) - Number of first reads trimmed for the aRNA primer (phv00222106.v6.p1)
aRNAPrimer(second) - Number of second reads trimmed for the aRNA primer (phv00222107.v6.p1)
aRNAPrimerRC(first) - Number of first reads trimmed for the reverse complement of aRNA primer (phv00222108.v6.p1)
aRNAPrimerRC(second) - Number of second reads trimmed for the reverse complement of aRNA primer (phv00222109.v6.p1)
AvgInpReadLen - Average read length (phv00222118.v6.p1)
AvgReadPerGeneExonic - Average number of reads that are exonic per gene (phv00222125.v6.p1)
AvgReadPerGeneIntronic - Average number of reads that are intronic per gene (phv00222278.v7.p1)
AvgUniqMapLen - Average read length for uniquely mapped reads (phv00222119.v6.p1)
BARCODE - Unique sequence that is part of the Illumina barcode (phv00222061.v6.p1)
BIOPSY_COMMENTS - Any comments from the surgeon who carried out the biopsy (phv00222023.v6.p1)
BIOPSY_ID - Identifier to indicate the samples collected from the same biopsy (phv00222017.v6.p1)
BLAST_Bacteria - Number of BLAST matches to Bacteria (phv00222080.v6.p1)
BLAST_ERCC - Number of BLAST matches to ERCC (phv00222088.v6.p1)
BLAST_Fish - Number of BLAST matches to Fish (phv00222081.v6.p1)
BLAST_Fly - Number of BLAST matches to Fly (phv00222082.v6.p1)
BLAST_HitsNotCounted - Number of BLAST matches to any other species (phv00222087.v6.p1)
BLAST_HitsNotTarget_or_ERCC - Percentage hits that map neither to the Human genome nor to ERCC sequences (phv00222079.v6.p1)
BLAST_Human - Number of BLAST matches to Human (phv00222083.v6.p1)
BLAST_Mouse - Number of BLAST matches to Mouse (phv00222084.v6.p1)
BLAST_Rat - Number of BLAST matches to Rat (phv00222085.v6.p1)
BLAST_TotalHits - The number of reads out of 5000 randomly selected reads that map against the nt database using BLAST (phv00222078.v6.p1)
BLAST_version - Blast version used (phv00222075.v6.p1)
BLAST_Yeast - Number of BLAST matches to Yeast (phv00222086.v6.p1)
BODY_SITE - Body site where sample was collected (phv00222019.v6.p1)
C1_ADDITIONAL_REAGENTS_ADDED - Additional reagents added besides the standard (phv00222039.v6.p1)
C1_CHIP - C1 Chip information (phv00222038.v6.p1)
C1_EXP_ID - Unique ID to identify samples that were collected using the same C1 experiment (if applicable) (phv00222036.v6.p1)
C1_SAMPLE_LOAD - Fresh/Frozen nuclei loaded on the C1 chip (phv00222037.v6.p1)
cDNA_BY - Code for the person who prepared the cDNA (phv00222049.v6.p1)
cDNA_DATE - CDNA preparation date (phv00222050.v6.p1)
CDS_RC(first) - Number of reads trimmed for the CDS 3' Adapter Reverse complement (phv00222116.v6.p1)
CDS(first) - Number of reads trimmed for the CDS 3' Adapter (phv00222115.v6.p1)
CELL_SUBCLASS - Specifies the cell sub-class. For instance: pyramidal, 5-HT, interneuron (phv00222054.v6.p1)
DEMULTIPLEXER - Demultiplexer used (phv00222032.v6.p1)
FastQC_version - FastQC version used (phv00222076.v6.p1)
FMAID - Foundational Model of Anatomy ID for the body site where the biopsy is taken from (phv00222020.v6.p1)
GencodeVersion - Gencode version (phv00222071.v6.p1)
HARVEST_METHOD - Method by which cells are harvested (phv00222046.v6.p1)
HARVEST_QUANT - Amount of RNA harvested (phv00222059.v6.p1)
HIGH_THROUGHPUT_SEQUENCER - High throughput sequencer used (phv00222029.v6.p1)
HTSeq_version - HTSeq version used (phv00222074.v6.p1)
HumanGenomeAssembly - Human Genome assembly used (phv00222070.v6.p1)
indexAdapter(first) - Number of first reads trimmed for the Index adapter (phv00222102.v6.p1)
indexAdapter(second) - Number of second reads trimmed for the Index adapter (phv00222103.v6.p1)
INPUT_AMOUNT - Input amount of RNA that goes in to library preparation (phv00222060.v6.p1)
IS_PAIRED? - Paired-end sequencing used? (phv00222031.v6.p1)
IS_polyA_SELECTED - Does the RNA go through poly(A) selection? (phv00222065.v6.p1)
IS_TUMOR - Tumor status (phv00222016.v6.p1)
LIBRARY_BY - Code for the person who prepared the library for sequencing (phv00222051.v6.p1)
LIBRARY_DATE - Library date (phv00222052.v6.p1)
MaxReadsPerGeneExonic - Maximum number of reads that are exonic per gene (phv00222126.v6.p1)
MaxReadsPerGeneIntronic - Maximum number of reads that are intronic per gene (phv00222279.v7.p1)
MULTI_FLOWCELLS? - Is the sample sequenced using multiple flowcells? (phv00222025.v6.p1)
MULTI_LANES? - Is the sample sequenced using multiple lanes? (phv00222024.v6.p1)
Multimapped - % Multimapped reads by STAR aligner (phv00222121.v6.p1)
nBelowPhredThreshold(first) - Number of first reads with Phred Score less than the threshold for at least one position (phv00222096.v6.p1)
nBelowPhredThreshold(second) - Number of second reads with Phred Score less than the threshold for at least one position (phv00222097.v6.p1)
nBothDiscarded - Number of read pairs discarded after trimming for being too short (< 20 nt) (phv00222093.v6.p1)
nBothTrimmed - Number of read pairs trimmed for contaminants (phv00222090.v6.p1)
NexteraXT_TransposaseRC(first) - Number of reads trimmed for 3' NexteraXT Transposase Reverse complement (phv00222114.v6.p1)
nFirstDiscarded - Number of first reads discarded after trimming for being too short (< 20 nt) (phv00222094.v6.p1)
nFirstTrimmed - Number of reads trimmed for contaminants (First reads) (phv00222091.v6.p1)
NGS_Protocol_FileName - Document that details the NGS processing pipeline applied to the SCAP-T samples (phv00222069.v6.p1)
NoExonicFeature - Number of reads that did not map to any exon as reported by HTSeq (phv00222127.v6.p1)
NoIntronicFeature - Number of reads that did not map to any intron as reported by HTSeq (phv00222280.v7.p1)
nSecondDiscarded - Number of second reads discarded after trimming for being too short (< 20 nt) (phv00222095.v6.p1)
nSecondTrimmed - Number of reads trimmed for contaminants (Second reads) (phv00222092.v6.p1)
nTotalReadPairs - Number of total reads from RNA-Sequencing (phv00222089.v6.p1)
nTSOFiltered(first) - Number of reads filtered for being the TSO primer concatemers (phv00222117.v6.p1)
NUM_PCR_CYCLES_cDNA - Number of PCR cycles used (phv00222063.v6.p1)
NUM_PCR_CYCLES_NEXTERA - Number of PCR cycles used (phv00222064.v6.p1)
NUMBER_aRNA_AMPLIFICATION_ROUNDS - Number of aRNA amplification rounds (phv00222062.v6.p1)
NumGenesExpressed - Number of genes with at least one exonic read (phv00222124.v6.p1)
NumGenesWithIntronicExpression - Number of genes with at least one intronic read (phv00222277.v7.p1)
OPERATOR - Code for the person who operated the sequencer (phv00222034.v6.p1)
PennSCAP-T_pipeline_version - Version of the Penn SCAP-T pipeline (phv00222072.v6.p1)
PROTOCOL_A_FILENAME - Protocol A Filename (If applicable) (phv00222041.v6.p1)
PROTOCOL_A_NAME - Protocol A Name (If applicable) (phv00222040.v6.p1)
PROTOCOL_B_FILENAME - Protocol B Filename (If applicable) (phv00222043.v6.p1)
PROTOCOL_B_NAME - Protocol B Name (If applicable) (phv00222042.v6.p1)
PROTOCOL_C_FILENAME - Protocol C Filename (If applicable) (phv00222045.v6.p1)
PROTOCOL_C_NAME - Protocol C Name (If applicable) (phv00222044.v6.p1)
PUTATIVE_CELL_TYPE - Specifies the cell class. For instance neuron, cardiomyocyte, brown adipose tissue, etc. (phv00222053.v6.p1)
READ_LENGTH - Read length (phv00222030.v6.p1)
ReadsCountedExonic - Number of reads counted by HTSeq as exonic (phv00222123.v6.p1)
ReadsCountedIntronic - Number of reads counted by HTSeq as intronic (phv00222276.v7.p1)
ReadsTooShort - % Reads too short and not mapped as reported by STAR aligner (phv00222122.v6.p1)
removed3N(first) - Number of first reads trimmed for Ns from 3' end (phv00222100.v6.p1)
removed3N(second) - Number of second reads trimmed for Ns from 3' end (phv00222101.v6.p1)
removed5N(first) - Number of first reads trimmed for Ns from 5' end (phv00222098.v6.p1)
removed5N(second) - Number of second reads trimmed for Ns from 5' end (phv00222099.v6.p1)
RIBOSOMAL_DEPLETION_KIT - Ribosomal depletion kit used (phv00222066.v6.p1)
RNASEQ_COMMENTS - Additional comments on the sequencing for the sample (phv00222035.v6.p1)
RNASEQ_GRP - ID that groups the samples that were sequenced on the same flowcell (phv00222026.v6.p1)
SAMPLE_HARVEST_BY - Code for the person who harvested the cells (phv00222047.v6.p1)
SAMPLE_HARVEST_DATE - Harvest date (phv00222048.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222068.v6.p1)
SAMPLE_ID - De-identified Sample ID (phv00222014.v6.p1)
Samtools_version - Samtools version used (phv00222077.v6.p1)
SEQ_CENTER - Sequencing Center (phv00222027.v6.p1)
SEQUENCING_DATE - Sequencing date (phv00222033.v6.p1)
SEQUENCING_PLATFORM - Sequencing platform (phv00222028.v6.p1)
SLICE_ID - Identifier to indicate the samples collected from the same slice of the biopsy (phv00222018.v6.p1)
SOURCE_REGION - Region of cell from where the input comes from (phv00222057.v6.p1)
SOURCE_TYPE - Cell source (phv00222055.v6.p1)
SOURCE_UNIT - Unit of source from where the sample material comes from (phv00222056.v6.p1)
SpikeInDilution - SpikeIn Dilution (phv00251846.v5.p1)
SpikeInType - SpikeIn Type (if it is used) (phv00251845.v5.p1)
STAR_version - STAR version used (phv00222073.v6.p1)
SURGEON - Randomly picked code for the surgeon who did the biopsy (phv00222021.v6.p1)
TREATMENT - Any special treatment that the cell went through - such as TIVA (phv00222058.v6.p1)
UniqMap - % Uniquely mapped reads by STAR aligner (phv00222120.v6.p1)
univAdapterRC(first) - Number of first reads trimmed for the reverse complement of the Universal adapter (phv00222104.v6.p1)
univAdapterRC(second) - Number of second reads trimmed for the reverse complement of the Universal adapter (phv00222105.v6.p1)