|
Status |
Public on Mar 01, 2020 |
Title |
Apoe 1M HFD |
Sample type |
SRA |
|
|
Source name |
ascending aorta
|
Organism |
Mus musculus |
Characteristics |
genotype: Apoe-/- diet: HFD
|
Treatment protocol |
mice were fed with HFD for 1 to 4 months
|
Extracted molecule |
total RNA |
Extraction protocol |
Digest the mice ascending aorta and sort GFP positive cells (smooth muscle cells) Libraries were prepared for sequencing at Yale using Chromium™ system (10x Genomics)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
|
|
Description |
ApoE mice feed with 1M HFD apoe_dko_1m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv
|
Data processing |
UMI-tools is used for the end to end processing of scRNA-Seq data Identified cell barcodes and UMI in the read sequence, which are then extracted from Read 1 and added to Read 2 read name. STAR,was used to map extracted reads from Read 2 to the reference mouse genome build 38 (GRCm38), followed by assigning reads to genes using featureCounts tool from the subread package (version 1.6.0). Quantification was performed using UMI-tools count function to find the number of unique UMIs mapping to each gene (GENCODE mouse annotation, release M15). Count data was filtered by: removing cells for which UMI count was less than 3,000 or total number of detected genes was less than 1,500; removing genes that were not expressed in less than or equal to 5% of the remaining cells in at least one sample ApoE and TGFβR2 UMI counts were removed from the processed data matrix Genome_build: GRCm38, version M15 (Ensembl 90) Supplementary_files_format_and_content: CSV files include raw and TMM values for all samples
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|
|
Submission date |
Nov 26, 2019 |
Last update date |
Mar 02, 2020 |
Contact name |
Michael Simons |
E-mail(s) |
michael.simons@yale.edu
|
Organization name |
Yale University
|
Department |
Department: Internal Medicine Cardiology
|
Lab |
Yale Cardiovascular Research Center
|
Street address |
3oo George St, Suite 773
|
City |
New Haven |
State/province |
CT |
ZIP/Postal code |
06511 |
Country |
USA |
|
|
Platform ID |
GPL21273 |
Series (2) |
GSE141031 |
Smooth muscle cell reprogramming in aortic aneurysms [scRNA-Seq] |
GSE141032 |
Smooth muscle cell reprogramming in aortic aneurysms |
|
Relations |
BioSample |
SAMN13389453 |
SRA |
SRX7217603 |