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| Status |
Public on Jun 24, 2016 |
| Title |
Donor number 7 live sorted cells, library 1 |
| Sample type |
SRA |
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| Source name |
human pancreas
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| Organism |
Homo sapiens |
| Characteristics |
cell type: live sorted cells
library: 1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and 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 |
D71
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| Data processing |
Paired end reads obtained by CEL-seq 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 mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. 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. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: hg19
Supplementary_files_format_and_content: D2_3_7_10_17.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 experiment (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 |
May 03, 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) |
| GSE81076 |
A single-cell transcriptome atlas of the human pancreas |
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| Relations |
| BioSample |
SAMN04939103 |
| SRA |
SRX1740281 |
| 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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