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| Status |
Public on Dec 11, 2017 |
| Title |
Fcx9 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
experiment: 20170314A
patient: 0006-YO
tissue: brain
brain region: Frontal Cortex
brodmann area: BA10
histology: Not specified
age: 49 years
Sex: Female
race: African American
source: U Miami Brain Endowment Bank
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cryofrozen post-mortem brain tissue was treated with nuclear extraction buffer, isolated nuclei was stained with DAPI and FACS purified.
Nuclei were loaded at the concentration of 100 nuclei/ml, and co-encapsulated in droplets with barcoded beads purchased from ChemGenes Corporation, Wilmington MA (Cat. # Macosko201110). When encapsulation was complete, droplets were heated to lyze the nuclei membrane, and were then broken by perfluorooctanol, following which beads were harvested, and hybridized RNA was reverse transcribed. Beads hybridized with RNA from individual nuclei was harvested, pooled and reverse transcribed. cDNA was then PCR amplified for 16 cycles with primer, buffer and cycle conditions identical to original Dropseq protocol and libraries were prepared by Nextera XT tagmentation according to Illumina's instructions and indexed with different Nextera index 1 primers
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
snDrop-seq data
[processed data file:]
FrontalCortex_snDrop-seq_UMI_Count_Matrix_04-07-2017.txt
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| Data processing |
Basecalls performed using bcl2fastq v2.17.1.14
First, paired-end reads were filtered out if read 1 had more than 4 non-T bases in the last 10 bases (to remove all non poly T-captured contaminated reads), or had one or more bases with poor quality score (less than 10). And cell barcode and UMI information were then inferred from the first 12 bases and the next 8 bases of read 1 respectively. The right mate of each read pair was trimmed to remove any portion of the SMART adaptor sequence or large stretches of polyA tails (6 consecutive bp or greater).
The trimmed reads were then aligned to the human genome (GENCODE GRCH38) using STAR v2.5 with the default parameter settings
Reads mapping to intronic or exonic regions of genes as per the GENCODE gene annotation were both recorded. One further correction step to fix barcode synthesis errors was performed by inserting N at last base of the cell barcode for reads which had identical first 11 bases of the cell barcode and same last T base of UMI.
Digital expression matrix was then generated with genes as rows and cells as columns. UMI counts were assigned for each gene of each cell by collapsing UMI reads which had only 1 edit distance
Genome_build: GENCODE GRCH38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each sample passing QC filtering. The README file on the series record contains where the adaptor information can be found and the script needed to generate the count matrices by cell barcode.
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| Submission date |
Apr 18, 2017 |
| Last update date |
Mar 18, 2022 |
| Contact name |
Kun Zhang |
| Organization name |
UCSD
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE97930 |
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain [snDrop-seq] |
| GSE97942 |
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain |
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| Relations |
| Reanalyzed by |
GSE198951 |
| BioSample |
SAMN06762452 |
| SRA |
SRX2742844 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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