|
| Status |
Public on Jun 14, 2020 |
| Title |
Sample_1498_201 |
| Sample type |
SRA |
| |
|
| Source name |
Leukocytes (PaxGene Tubes)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood
gender: female
group/diagnosis: Unaffected sibling
batch: Batch_2
rin: 7.7
family id: Family_1498
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified in accordance with the PAX gene RNA kit per manufacterer's instructions. Globin mRNA was depleted from samples using GLOBINclear - Human Kit (Life Technologies, USA).
RNA libraries were prepared for sequencing using stranded Illumina Tru-Seq protocols using the Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina adapter sequences were trimmed from all fragmented reads using TrimGalore (options –paired –illumina) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
All high-quality trimmed reads were mapped to UCSC Homo sapiens reference genome (build hg37) using default STAR v2.4.0 parameters.
Samtools was used to convert bamfiles to samfiles and featureCounts was used to quantify gene expression levels for each individual sample using default paired-end parameters.
Genome_build: hg37/hg19
Supplementary_files_format_and_content: Raw count data were generated with featureCounts and are provided as a separate matrix.
|
| |
|
| Submission date |
Jun 13, 2020 |
| Last update date |
Jun 15, 2020 |
| Contact name |
Michael S Breen |
| Organization name |
Ichan School of Medicine at Mount Sinai
|
| Department |
Depts. of Psychiatry, Genetics and Genomic Sciences
|
| Street address |
1468 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE152421 |
Episignatures stratifying ADNP syndrome show modest correlation with phenotype [RNA-seq] |
| GSE152428 |
Episignatures stratifying ADNP syndrome show modest correlation with phenotype |
|
| Relations |
| BioSample |
SAMN15230345 |
| SRA |
SRX8541096 |
