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| Status |
Public on Jul 17, 2020 |
| Title |
Cck_1nM_1 |
| Sample type |
SRA |
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| Source name |
Pancreatic acinar cells
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Pancreas
cell line: AR42J
treatment: 1nM CCK
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| Treatment protocol |
Cells were incubated in growth medium with the different 5 concentrations of CCK/insulin or with growth medium only in triplicates for 24 hours.
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| Growth protocol |
Cells were thawed and let to recover for a week before exposed to CCK or insulin. Growth medium used was low-glucose DMEM, 10% FBS, 1% Pen/strep, 1% NEAA, 1% Glutamine.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
cells were lysed in TRI reagent for RNA extraction. RNA was isolated by Direct-zol RNA MiniPrep kit.
Bulk analysis, mcSCRBseq protocol was used (Bagnoli et al., 2018)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
Bulk_RNA_mcSCRBseq
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| Data processing |
bcl2fastq/2.15.0.4. sample demultiplexing was provided to obtain sample specific reads in two fastq files (read 1 (R1) and read 2 (R2))
To obtain the UMI counts, fastq reads were aligned to the rat reference genome (Rnor_6.0.96) using zUMI package (Parekh et al., 2018).
Genome_build: Rnor_6.0.96
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule UMI count values for each Sample
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| Submission date |
Jul 16, 2020 |
| Last update date |
Jul 17, 2020 |
| Contact name |
Keren Bahar-Halpern |
| Organization name |
Weizmann Institute
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| Lab |
Itzkovitz
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| Street address |
Herzl St 234
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL25029 |
| Series (1) |
| GSE154533 |
Zonation of pancreatic acinar cells in diabetic mice |
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| Relations |
| BioSample |
SAMN15548225 |
| SRA |
SRX8742804 |
| 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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