|
| Status |
Public on Dec 04, 2018 |
| Title |
6_Cas9-3 |
| Sample type |
SRA |
| |
|
| Source name |
striatal tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: striatal tissue
treatment (viral injection): Cas9
age: 3 weeks-old
|
| Treatment protocol |
Injected with adeno-associated virus into the striatum.
|
| Growth protocol |
3-month old wild type mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNAeasy Mini Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
Libraries were prepared on cDNA generated using Clontech SmartER kits. Illumina adapters were ligated using the NexteraXT DNA kit for Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
6_Cas9-3_alaHtseq.txt
|
| Data processing |
Reads were aligned to an assembly of Mus musculus (house mouse) (Genome Reference Consortium Mouse Build 38 patch release 3 (GRCm38.p3)) using STAR software (v2.5.2b).
Transcripts were annotated with GENCODE M3 release
unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.3.3.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Nov 01, 2018 |
| Last update date |
Dec 04, 2018 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE122072 |
Shortening the half-life of Cas9 maintains its gene editing ability and reduces neuronal toxicity |
|
| Relations |
| BioSample |
SAMN10359411 |
| SRA |
SRX4965982 |
