|
| Status |
Public on Sep 21, 2017 |
| Title |
LV_control_M3_exp1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
cohort: Uninfected
days post infection: 0
mouse id: M3
experiment id: exp1
sequencing batch: 5
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For whole organs, samples were lysed in Trizol and total RNA was extracted by phenol-chloroform extraction followed by purification with Dynabeads MyOne Silane beads (Thermoscientific). For sorted cell populations, CD8+ T cell populations (5,000-10,000 cells per sample) were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol and total RNA was extracted with Dynabeads MyOne Silane beads. After bead-based enrichment, total RNA samples were purified by on-bead DNase I treatment followed by cleanup with 80% ethanol. RNA concentration was normalized across samples prior library construction.
Total RNA was heat-fragmented to an average size of 500 bp fragments and reverse transcribed with barcoded oligo(dT) primers containing an Illumina-compatible adapter sequence. After RNA degradation, barcoded, single-stranded cDNA samples were pooled and flanked by an Illumina-compatible adapter sequence in their 3’ end using a ‘primer extension’ method with DNA Pol I, Large Klenow Fragment exo minus. cDNA pools flanked on both ends with illumina sequences were then amplified by PCR and sequenced on Illumina sequencers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Whole tissue
raw_counts_exp1_day7_day21.txt
|
| Data processing |
Fastq files were demultiplexed with custom scripts and quality checked with FastQC.
Read mapping using STAR aligner with mm10 genome.
FeatureCounts was used to count mapped reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample. Rows = genes, and columns = whole-tissue or sorted CD8+ cell samples.
|
| |
|
| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolas Chevrier |
| E-mail(s) |
nchevrier@uchicago.edu
|
| Organization name |
The University of Chicago
|
| Department |
Pritzker School of Molecular Engineering
|
| Lab |
Nicolas Chevrier
|
| Street address |
5640 South Ellis Avenue
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE87633 |
Organism-level analysis of vaccination reveals networks of protection across tissues |
|
| Relations |
| BioSample |
SAMN06857335 |
| SRA |
SRX2773210 |
