|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jul 17, 2020 |
Title |
Cck_1µM_3 |
Sample type |
SRA |
|
|
Source name |
Pancreatic acinar cells
|
Organism |
Rattus norvegicus |
Characteristics |
tissue: Pancreas cell line: AR42J treatment: 1µM CCK
|
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.
|
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.
|
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)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
|
|
Description |
Bulk_RNA_mcSCRBseq
|
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
|
|
|
Submission date |
Jul 16, 2020 |
Last update date |
Jul 17, 2020 |
Contact name |
Keren Bahar-Halpern |
Organization name |
Weizmann Institute
|
Lab |
Itzkovitz
|
Street address |
Herzl St 234
|
City |
Rehovot |
ZIP/Postal code |
7610001 |
Country |
Israel |
|
|
Platform ID |
GPL25029 |
Series (1) |
GSE154533 |
Zonation of pancreatic acinar cells in diabetic mice |
|
Relations |
BioSample |
SAMN15548232 |
SRA |
SRX8742797 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|