|
| Status |
Public on Aug 07, 2019 |
| Title |
B1: RNAseq (paired-end sequencing) |
| Sample type |
SRA |
| |
|
| Source name |
resting state B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6
origin: Spleen
cell type: resting state B cells
|
| Growth protocol |
Cells were isolated using Miltenyi magnetic sorting kit and cultured for 2 hours in complete RPMI medium at 37ºC, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cells, subjected to library preparation and sequencing in illumina platform.
TruSeq RNA Sample Preparation v2 Guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq quality was determined by FASTQC in Galaxy server
Adapter removal was done for Riboseq data using Clip (FastX-tool kit) in galaxy server
Riboseq reads were further trimmed using Trim in galaxy server
Riboseq data was aligned to ribosomal mouse RNA sequences (custom genome file) using bowtie 2 in galaxy server and only the reads that dd not align were used for further analysis.
Reads not aligned to mouse genome (mm10) using tophat in galaxy server.
htseq-count in galaxy server was used to count the reads per gene. GTF file from ensembl modified to match the ucsd genome was used for counting.
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: Tabular format with read counts per gene (created using htseq-count.
|
| |
|
| Submission date |
Mar 14, 2019 |
| Last update date |
Aug 07, 2019 |
| Contact name |
G Aneeshkumar Arimbasseri |
| E-mail(s) |
aneesh@nii.ac.in
|
| Phone |
+91 9971986746
|
| Organization name |
National Institute of Immunology
|
| Department |
Molecular Genetics Laboratory
|
| Lab |
Molecular Genetics Laboratory
|
| Street address |
Aruna Asaf Ali Marg
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE128298 |
Translatome and transcriptome analysis of resting B and T cells from mice |
|
| Relations |
| BioSample |
SAMN11126098 |
| SRA |
SRX5521597 |
