|
| Status |
Public on May 17, 2016 |
| Title |
D4 |
| Sample type |
SRA |
| |
|
| Source name |
Monocyte derived macrophages isolated from ipsilateral hemisphere of mouse brains 1 day after TBI
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: monocyte-derived macrophage
cell surface markers: CD45hiLy6G-CD11b+F480+
sample type: single cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Monocyte-derived macrophages isolated from ipsilateral brain tissues were isolated by FACS on an AriaII. Total RNA was isolated, converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols. cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Samples are essentially "identical" (FACS purified cells, then run on a C1 for single cell RNAseq), and defined by the flow cytometry gating strategy provided.
|
| Data processing |
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2 and read quality assessed using FastQC
Gene expression modeled using RSEM version 1.2.21 with Bowtie2 2.2.3 for read alignment. Default parameters were used.
Genome_build: Release GRCm38 of the mouse genome
Supplementary_files_format_and_content: Tab delimited text files showing TPM for all genes
|
| |
|
| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Charlie Kim |
| E-mail(s) |
cckim47@gmail.com
|
| Organization name |
University of California, San Francisco
|
| Department |
Medicine
|
| Lab |
Kim
|
| Street address |
1001 Potrero Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE79510 |
Single-cell RNA sequencing reveals non-canonical brain macrophage activation states in murine neurotrauma |
|
| Relations |
| BioSample |
SAMN04574113 |
| SRA |
SRX1655515 |
