|
| Status |
Public on Jan 05, 2016 |
| Title |
islet_single_cell_63 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islet
|
| Organism |
Homo sapiens |
| Characteristics |
assigned cell type: beta
qc pass: TRUE
cell count: 1
ercc_mix: mix2
ercc_dilution: 1000000
|
| Treatment protocol |
Islets were cultured in CMRL medium (Life technology) supplemented with 10% FBS, 2 mM glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
To disassociate islets into single cells, islets were incubated in Accutase (Life technology) in 37 °C for 20 min, neutralized by CMRL medium. Purification of single cells was performed by flow cytometry cell sorting on a Moflo AstriosEQ (Beckman Coulter, Miami)
cDNA synthesis and enrichment was performed following the Smart-seq2 protocol as described (Picelli et al., 2014).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimming of adapter sequences was performed with trimmomatic (v 0.32) minimum read length after trimming: 25
Alignment of the trimmed reads to the human transcriptome (hg19 GRCh37 ftp://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.74.cdna.all.fa.gz) was performed with bowtie1 (v 1.1)
Calculation of normalized transcript-wise expression estimates (RPKM values) was performed based on the transcriptome alignments using the R (v 3.1.2) package BitSeq (v 1.10.0). Function: getExpression() with uniform=FALSE
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include transcript-wise RPKM values or read counts for each sample
|
| |
|
| Submission date |
Oct 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE73727 |
Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes |
|
| Relations |
| BioSample |
SAMN04145815 |
| SRA |
SRX1304205 |
