|
| Status |
Public on Aug 03, 2018 |
| Title |
RNA_Esamhi_WT_2 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: dendritic cells
tissue: spleen
dc_subset: Esamhi
genotype: WT
replicate: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were resuspended in Trizol LS and RNA was extracted using the Arcturus PicoPure kit (Thermo Fisher Scientific).
cDNA libraries were prepared using the SMART-seq v4 Ultra Low Input RNA kit and Low Input Library Prep kit (Life Sciences). Libraries were prepared for sequencing using HiSeq SBS v4 Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
BCL files were converted to fastq files using bcl2fastq2 Conversion Software ( v2.17)
Single-end RNA-seq reads from were trimmed to remove low quality reads using Trimmomatic (v.0.36)
Trimmed reads were mapped to the Mus musculus genome (mm10 assembly) using Bowtie2 (v2.2.9).
Reads were counted in exon regions using the summarizeOverlaps function within the GenomicAlignments R package (v1.10.1 )
Genome_build: mm10
Supplementary_files_format_and_content: Table of annotated raw counts using the UCSC mm10 knownGene model.
|
| |
|
| Submission date |
Nov 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Colleen Lau |
| Organization name |
Cornell University
|
| Department |
Microbiology & Immunology
|
| Street address |
930 Campus Road
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106406 |
Transcription factor Etv6 controls functional differentiation of cross-presenting classical dendritic cells [RNA-Seq] |
| GSE106408 |
Transcription factor Etv6 controls functional differentiation of cross-presenting classical dendritic cells |
|
| Relations |
| BioSample |
SAMN07964500 |
| SRA |
SRX3350456 |
