|
| Status |
Public on Oct 28, 2016 |
| Title |
Control 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebellar Purkinje neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 4-weeks-old
tissue: brain
genotype/variation: Pcp2-BacTrap; Rbm17 f/+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
BacTRAP profiling was performed as previously described (Heiman et al. 2014) with the following modifications: One cerebellum was homogenized in 1.5 mL of homogenization buffer and 60 µg each of 19C8 and 19F7 was used for every immunoprecipitation experiment.
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ribosome-bound RNA, BacTRAP technique
ZL37881
|
| Data processing |
Alignment: TopHat v2.1.0 using --mate-inner-dist of 200 and rest default settings
Counts: Htseq version 0.6.0 using default settings
Genome_build: mm10
Supplementary_files_format_and_content: Counts_Matrix.txt: Read count matrix from Htseq.
Supplementary_files_format_and_content: bed: Junction bed files from Tophat output.
|
| |
|
| Submission date |
Mar 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhandong Liu |
| E-mail(s) |
zhandonl@bcm.edu
|
| Phone |
8328248878
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1250 Moursund St., STE NR-1325
|
| City |
Houston |
| State/province |
TEXAS |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE79020 |
Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models |
|
| Relations |
| SRA |
SRX1620342 |
| BioSample |
SAMN04539770 |
