|
| Status |
Public on Aug 12, 2020 |
| Title |
Ldlr_null_Donor_into_WT_sample_3 |
| Sample type |
SRA |
| |
|
| Source name |
Ldlr null donor macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed WT CD45.1 diabetic mice.
|
| Organism |
Mus musculus |
| Characteristics |
cell type: macrophage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared for sequencing using the NuGEN Ovation RNA-Seq system v2 reagents.
The Ovation Ultralow DR Multiplex system was used for for the adapter ligation step.
Libraries were amplified by 9 cycles, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
112
|
| Data processing |
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Fastq files were trimmed of low quality bases and adapters with Trimmomatic
Reads were mapped to the genome with Bowtie 2.1.0 Tophat 2.0.0 and HTSeq 0.6.1 .
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw counts for each gene
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Richard A Friedman |
| Organization name |
Columbia University Irving Medical Center
|
| Department |
Medicine
|
| Lab |
Cancer Center
|
| Street address |
1130 St. Nicholas Av
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE142204 |
Effect of RAGE on macrophage transcriptome in regression of diabetic atherosclerosis |
|
| Relations |
| BioSample |
SAMN13615153 |
| SRA |
SRX7397596 |
