|
| Status |
Public on Mar 15, 2019 |
| Title |
2days pbs line 3348A [D5-3] |
| Sample type |
SRA |
| |
|
| Source name |
2days pbs_lungs
|
| Organism |
Mus musculus |
| Characteristics |
collaborative cross (cc) line: 3348A
infected with: PBS (control)
weight loss: -0.543478261
viral load: 75.3837642
tissue: lungs
time point: 48h after infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Murine lungs were harvested immediately after the time of sacrifice, sliced into small pieces, homogenized using BeadBlaster Microtube Homogenizer (90sec, 4000rpm) in the presence of QIAzol, and used for total RNA extraction using the miRNeasy Mini Kit.
For the preparation of RNA‐Seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95°C) treatment for 4:30 min (NEBNext Magnesium RNA Fragmentation Module). The 3′ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen). Strand‐specific cDNA was synthesized using a poly T‐VN oligo (18 T) and Affinity Script RT enzyme (Agilent). Double‐strand DNA was obtained using Second strand synthesis kit (NEB). DNA ends were repaired using T4 polynucleotide kinase and T4 polymerase (NEB‐Next). After the addition of an adenine base residue to the 5′ end using Klenow enzyme (NEB‐Next), a barcode Illumina compatible adaptor (IDT) was ligated to each fragment. The washed DNA fragment was amplified by PCR (12 cycles) using specific primers (IDT) to the ligated adaptors. The quality of each library was analyzed by TapeStation (Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: countsFinal.txt; countsNormFinal.txt
|
| Data processing |
bcl2fastq/2.15.0.4 software used for basecalling.
Reads were aligned using the HISAT aligner to the mouse reference genome (NCBI 37, mm9).
Expression levels of the list of mouse genes were then calculated and normalized by the total number of mapped reads per experiment, using HOMMER with the default parameters.
Recorded are those reads that were mapped to mouse gene exons (using the UCSC transcript annotation).
Reads that were mapped to multiple positions were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized reads by the total number of mapped reads per experiment
|
| |
|
| Submission date |
Apr 23, 2018 |
| Last update date |
Mar 15, 2019 |
| Contact name |
Amit Frishberg |
| E-mail(s) |
[email protected]
|
| Organization name |
Tel-Aviv University
|
| Department |
Cell Research & Immunology
|
| Lab |
Gat-Viks
|
| Street address |
Haim Levanon
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE113530 |
Cell composition analysis of bulk genomics using single cell data |
|
| Relations |
| BioSample |
SAMN08971126 |
| SRA |
SRX3988517 |
