|
| Status |
Public on Aug 07, 2019 |
| Title |
T2: Riboseq (single-end sequencing |
| Sample type |
SRA |
| |
|
| Source name |
resting state T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6
origin: Spleen
cell type: resting state T cells
|
| Treatment protocol |
Treated with 100µg/ml cycloheximide for 15 minutes before harvesting
|
| 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 cell lysate was treated with a mixture of ribonuclease (RNaseA, Rnase T1, S7 nuclease) and monosomes were isolated. RNA from monosomes were used for library preparation.
Ribosome profiling protocol as described in "Ingolia, N.T., Brar, G.A., Rouskin, S., Mcgeachy, A.M., and Weissman, J.S. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550."
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: Riboseq
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 |
GPL19057 |
| Series (1) |
| GSE128298 |
Translatome and transcriptome analysis of resting B and T cells from mice |
|
| Relations |
| BioSample |
SAMN11126099 |
| SRA |
SRX5521596 |
