|
| Status |
Public on Apr 01, 2023 |
| Title |
13m_ICH_R-mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Rat brain tissues
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: contralateral brain
age: 13 mon old
disease: intracerebral hemorrhage
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from nine rat brains by using TRIzol Reagent (Ambion), and then pooled together an equal amount of total RNA from all samples to obtain the represented RNA mix. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (invitrogen) before being used for directional RNA-seq library preparation. Purified mRNAs were ion fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequenceand randomized hexamer. The cDNAs were purified and amplified. And products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with Pvalue < =0.01 and Fold change >=2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
Apr 01, 2023 |
| Contact name |
dong chen |
| Organization name |
ablife
|
| Street address |
GaoXin 2nd Road
|
| City |
wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE106924 |
High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. [RNA-Seq] |
| GSE106952 |
High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. |
|
| Relations |
| BioSample |
SAMN08031751 |
| SRA |
SRX3398022 |
