|
| Status |
Public on Aug 20, 2017 |
| Title |
wt2 (cryaa-R49C WT2) |
| Sample type |
SRA |
| |
|
| Source name |
Lens
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
postnatal age: 2-day-old
genotype/variation: wild-type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library preparation was performed using a Clontech poly-A kit according to the manufacturer’s protocol. The resulting cDNA was then blunt ended, an A base was added to the 3’ ends, and Illumina sequencing adapters were ligated to the ends. The ligated fragments were then amplified for 12 cycles using primers that incorporated unique index tags and the resulting fragments were sequenced on an Illumina HiSeq 2500 sequencing system using single reads extending 50 bases and targeting 30M reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed with Casava v1.8
Reads were aligned to Ensembl GRCm38.76 with STAR v2.0.4b
Gene counts were produced with Subread:featureCounts v1.4.5 and transcript/isoform counts were estimated with Sailfish v0.6.3
Genome_build: GRCm38.76
Supplementary_files_format_and_content: gene count text file
|
| |
|
| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Usha Andley |
| E-mail(s) |
andley@vision.wustl.edu
|
| Phone |
314-362-7167
|
| Organization name |
Washington University School of Medicine
|
| Department |
Ophthalmology and Visual Sciences
|
| Lab |
Andley
|
| Street address |
660 S. Euclid Avenue
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE98027 |
Changes in gene expression due to alpha-crystallin mutations cryaa-R49C and cryab-R120G in mutant knock-in mouse lenses |
|
| Relations |
| BioSample |
SAMN06771444 |
| SRA |
SRX2749423 |
