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Sample GSM7291493 Query DataSets for GSM7291493
Status Public on May 08, 2023
Title NF1MEC2
Sample type SRA
 
Source name MECs
Organism Rattus norvegicus
Characteristics tissue: MECs
genotype: wildtype
Extracted molecule total RNA
Extraction protocol For RNA extraction of whole fat pads and tumors, fresh harvested samples were cut up and added to MPbio lysing matrix E tube. Cells were homogenized for 20 seconds in an MPbio homogenizer, then RNA was isolated from the supernatant using the Trizol-chloroform-isopropanol RNA extraction method. For RNA extraction of mature adipocytes, RNA was isolated using the Trizol-chloroform-isopropanol RNA extraction method. For RNA extraction of cultured epithelial cells and fibroblast, 1.2105 cells were plated into one well of a six-well plate. At 90-100% confluency, RNA was isolated using QIAGEN QIAshredder and RNeasy Kit manufacturer’s instructions.
Libraries were prepared by the Van Andel Institute Genomics Core from 500 ng of total RNA using the KAPA mRNA Hyperprep kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).Individually indexed libraries were pooled and 50 bp, paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2 sequencing kit (Illumina Inc., San Diego, CA, USA) to an average depth of 45M reads per sample. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description wildtype MECs
Data processing Raw reads were trimmed of sequencing adapters with Trim_Galore
Trimmed reads were mapped to Rnor 6.0 assembly with STAR v2.5.2b using options ‘--twopassMode Basic’ and ‘--quantMode GeneCounts’ to directly output counts for all features from the ensemble annotation 6.0.90
Assembly: Rnor 6.0
Supplementary files format and content: raw_counts.tsv has the raw counts output from STAR mapping for features in the ensemble 6.0.90 annotation.
 
Submission date May 03, 2023
Last update date May 08, 2023
Contact name Ian Beddows
Phone 000000000
Organization name Van Andel Institute
Street address 333 Bostwick
City Grand Rapids
State/province MI
ZIP/Postal code 49503
Country USA
 
Platform ID GPL25947
Series (1)
GSE231603 Nf1 Deficiency Increases Mammary Collagen Deposition and Restricts Adipocyte Differentiation Before Tumor Formation
Relations
BioSample SAMN34570882
SRA SRX20210146

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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