|
| Status |
Public on Jul 04, 2019 |
| Title |
3496-SP-4 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: FACS-purified pro-B
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow was isolated, CD19+ cells were enriched by MACS (Miltenyi), and pro-B and large pre-B cells were FACS-purified into PBS and processed for RNA using the QIAGEN Rneasy Mini Kit (Cat. #74104); 20-50 ng of total RNA was prepared for sequencing
Prepared using Illumina's TruSeq Stranded mRNA kit (Cat. #20020595) per manufacturer instructions with mRNA enriched via poly-A selection using oligoDT beads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
poly-A enriched RNA
|
| Data processing |
RTA (version 2.7.6; Illumina) was used for base calling
Analysis was completed using MultiQC v1.2
On paired fastq files, transcript abundance was estimated, and these read counts were imported into edgeR for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains read counts for each sample
|
| |
|
| Submission date |
Jun 03, 2019 |
| Last update date |
Jul 04, 2019 |
| Contact name |
Matthew Stier |
| E-mail(s) |
stiermt@gmail.com
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Internal Medicine
|
| Lab |
B1227 MCN
|
| Street address |
1161 21st Avenue South
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE132123 |
Transcriptome Analysis of IL-33-Deficient Early Developing B Cells |
|
| Relations |
| BioSample |
SAMN11942478 |
| SRA |
SRX5960780 |
