|
| Status |
Public on Jul 15, 2016 |
| Title |
Bcell-marginal-R13 |
| Sample type |
SRA |
| |
|
| Source name |
Marginal Zone B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6JNimr
tissue: Spleen
age: 7-9 weeks
Sex: Female
immunization: None
flow strategy: B220+AA4.1-Cd23-IgMhigh
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Female mouse C57BL/6 B cell populations were sorted on BD FACSAriaII, BD Influx or Beckman Coulter MoFlo XDP cell sorters; collected cells were centrifuged and ressuspended in Trizol and RNA was extracted with the Rneasy kit (Qiagen) according to the manufacturer's instructions
Libraries were prepared with Illumina's TruSeq stranded mRNA Sample Preparation kit according to the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PolyA+ RNA
|
| Data processing |
fastq files were created with CASAVA 1.8.1
Sequenced reads were mapped to mm10 using STAR version 2.3.0e with parameters --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The number of reads mapping to protein coding gene annotations from Ensembl version 72 and de novo assembled lncRNA annotations from the current study was determined using featureCounts (Subread version 1.4.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited count matrix containing raw read counts for
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jethro Johnson |
| E-mail(s) |
jethro.johnson@jax.org
|
| Organization name |
Jackson Laboratory for Genomic Medicine
|
| Lab |
Weinstock Lab
|
| Street address |
10 Discovery Drive
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE72018 |
Long non-coding RNAs in B cells (RNA-Seq) |
| GSE72019 |
Long non-coding RNAs in B cells |
|
| Relations |
| BioSample |
SAMN03983963 |
| SRA |
SRX1144010 |
