|
| Status |
Public on Feb 11, 2019 |
| Title |
R42016-105pf_39-IR_L2 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Homo sapiens |
| Characteristics |
mgs_level: 2
age: 70
Sex: F
rin: 7.8
pmi: 16.23
tissue: retina punch
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Retina punches flash frozen in liquid nitrogren and stored in -80 C; retina homogenized and RNA isolated with TRIZol® protocol with additional washing steps
Randomized to batches and constructed with TruSeq® Stranded mRNA Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptors with Trimmomatic 0.36 and quality of raw FASTQs were checked with FastQC.
Reads were aligned to reference genome with STAR 2.5.2a.
Aligned reads were quantified as expacted counts at transcript level and collapsed to gene level using RSEM 1.2.31
Genome_build: GRCh38.p3/ENSEMBLv82
Supplementary_files_format_and_content: RSEM_gene_counts.tsv (tab delimited value file with raw gene counts)
Supplementary_files_format_and_content: Normalized_CPM.txt (tab delimited value file with normalized counts per million expression values)
Supplementary_files_format_and_content: DE_analysis.txt (space delimited value file with differential expression output)
|
| |
|
| Submission date |
Jun 14, 2018 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Matthew J Brooks |
| E-mail(s) |
[email protected]
|
| Phone |
301-443-4906
|
| Organization name |
NIH
|
| Department |
NEI
|
| Lab |
NNRL
|
| Street address |
6 Center Dr Bldg 6, Rm 303
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE115828 |
Integrated analysis of genetic variants regulating retinal transcriptome (GREx) identifies genes underlying age-related macular degeneration |
|
| Relations |
| BioSample |
SAMN09427643 |
| SRA |
SRX4331185 |
