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Sample GSM4672969 Query DataSets for GSM4672969
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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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