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Status |
Public on Jan 19, 2017 |
Title |
islet_single_cell_artemether_16 |
Sample type |
SRA |
|
|
Source name |
pancreatic islet
|
Organism |
Homo sapiens |
Characteristics |
assigned cell type: delta treatment length: 24 cell count: 1 ercc_mix: mix1 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. Artemether treatment was administered for the indicated period of time.
|
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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
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
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|
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Submission date |
Jul 22, 2016 |
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 |
GPL21290 |
Series (1) |
GSE84714 |
Artemisinins target GABA receptor signaling to induce alpha to beta cell transdifferentiation |
|
Relations |
BioSample |
SAMN05430155 |
SRA |
SRX1970468 |