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| Status |
Public on Apr 23, 2023 |
| Title |
Brain, BDL1 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: post natal day 60
protocol: bile duct ligation (BDL)
bdl modeling time: 4 weeks
tissue: brain
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| Treatment protocol |
The AAVs were prepared in phosphate-buffered saline (PBS) with a concentration of 1.5 x 1011 GC/rat in a total volume of 20 μl. A 30-gauge needle connected with a PE10 tube filled with AAV solution was inserted 3 mm deep into the cisterna magna. A 20 μl of solution was injected into the cisterna magna at a rate of 1.6 μl/min (1.5 x 1011 GC/rat in both groups) by a 50 μl syringe (Hamilton Company, Reno, NV) using a syringe pump (Harvard Apparatus, Holliston, MA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw fastq files were assessed for quality before and after trimming adaptors using the FastQC software. Using Trimmomatic 0.36, reads with a minimum length of 50 bp and a Phred quality score >30 were finally retained
Indexes were constructed for a genome file and the reads were aligned to the reference genome using HISAT2
The number of the fragments mapped to each gene was calculated using the featureCounts command
Genome_build: RGSC 6.0/rn6
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample
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| Submission date |
Apr 23, 2020 |
| Last update date |
Apr 23, 2023 |
| Contact name |
Chihao Zhang |
| E-mail(s) |
chihao.zhang@yale.edu
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| Organization name |
Yale University
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| Department |
Internal Medicine
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| Lab |
Iwakiri Lab
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| Street address |
300 Cedar Street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE149227 |
RNA-seq analysis of brain tissue treated by VEGFC in BDL-induced cirrhotic rat with hepatic encephalopathy |
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| Relations |
| BioSample |
SAMN14680953 |
| SRA |
SRX8166985 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4494600_B17B2.txt.gz |
89.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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