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| Status |
Public on Oct 04, 2016 |
| Title |
Donor D28, live sorted cells, library 2 |
| Sample type |
SRA |
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| Source name |
human pancreas
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| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreas
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by an automated version of the previously described Cel-Seq2 technique. Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
D28-2
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| Data processing |
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: hg19
Supplementary_files_format_and_content: cellsystems_dataset_4donors.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the originating donor (D*) and the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
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| Submission date |
Aug 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mauro Muraro |
| E-mail(s) |
m.muraro@scdiscoveries.com
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| Organization name |
Single Cell Discoveries
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| Street address |
Uppsalalaan, 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE85241 |
A single-cell transcriptome atlas of the human pancreas [CEL-seq2] |
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| Relations |
| BioSample |
SAMN05513826 |
| SRA |
SRX2003935 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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