|
| Status |
Public on Nov 20, 2023 |
| Title |
splenic marginal zone B cell, WT, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
splenic marginal zone B cell (CD19+, CD23-, CD21 high)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: splenic marginal zone B cell (CD19+, CD23-, CD21 high)
genotype: Wild-type
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were prepared using the Direct-zol RNA Miniprep (Zymo Research) and 1mg of total RNA was used for the construction of sequencing libraries.
The TruSeq Stranded mRNA Library prep kit was used for construction of cDNA libraries for RNA-sequencing (Illumina). The cDNA libraries were ligated with indexed primers and amplified by PCR for 10 cycles, multiplexed and sequenced in house with an Illumina NextSeq550 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment to the mouse mm10 assembly was conducted by STAR 5.02 (Dobin et al., 2013) on the DNAnexus platform
Normalization and differential expression by DESeq2 were performed through a HOMER v4.10.4 implementation of the package in R.
Assembly: mm10
|
| |
|
| Submission date |
Jul 18, 2023 |
| Last update date |
Nov 20, 2023 |
| Contact name |
Katia Georgopoulos |
| E-mail(s) |
katia.georgopoulos@cbrc2.mgh.harvard.edu
|
| Phone |
617-7264445
|
| Organization name |
Harvard Medical School
|
| Department |
CBRC
|
| Lab |
Georgopoulos
|
| Street address |
1st and 13th St
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE232490 |
A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS |
| GSE237725 |
A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [RNA-Seq 3] |
|
| Relations |
| BioSample |
SAMN36536638 |
| SRA |
SRX21075809 |
