|
| Status |
Public on Nov 01, 2022 |
| Title |
hepatocyte rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: C57BL6
treatment: No treatment
selection: No selection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA lysis buffer is TRIzol reagent
RNA libraries were prepared with standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Selection_Customcount2.txt
|
| Data processing |
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Custom bowtie indexes were built containing the gene targets for custom sequence integration.
Libraries were aligned to these custom indexes using bowtie 1.0.0 using a 50 base wide sliding window. The window was offset in 15 base steps along the sequence reads until an alignment was found or the end was reached. This allowed us to place the integrated sequence relative to specific genes from the reference genome and verify that it was at the expected integration site.
These windowed alignments were parsed to generate the matrix of unique counts provided as processed data.
Assembly: mm9
Supplementary files format and content: text file includes matrix of unqiue counts using the custom index alignment for integrated sequences
|
| |
|
| Submission date |
Oct 31, 2022 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Amita Tiyaboonchai |
| E-mail(s) |
tiyaboon@ohsu.edu
|
| Organization name |
Oregon Health & Science University
|
| Department |
Pediatrics
|
| Street address |
3181 SW Sam Jackson Park Rd.
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE216550 |
Self-cleaving guide RNAs enable pharmacological selection of precise gene editing events in vivo |
|
| Relations |
| BioSample |
SAMN31537111 |
| SRA |
SRX18092486 |
