|
| Status |
Public on Sep 11, 2019 |
| Title |
P54 [discovery] |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
acr at 3m: Yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole blood of kidney transplant recipients 3 months post-transplantation.
The library was generated standard TruSeq mRNA library generation kit (Illumina Inc).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Standard mRNA library.
Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation, and mRNA sequencing was performed on an Illumina HiSeq2000 sequencer.
|
| Data processing |
The reads with good quality were firstly aligned to human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering for reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription level across samples, followed by quantile normalization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include quantile-normalized counts.
|
| |
|
| Submission date |
Sep 24, 2018 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Weijia Zhang |
| E-mail(s) |
weijia.zhang@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Renal
|
| Lab |
Bioinfomatics
|
| Street address |
1 Gustave L. Levy Pl
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE120396 |
A peripheral blood gene expression signature diagnoses subclinical acute rejection [discovery] |
| GSE120398 |
A peripheral blood gene expression signature diagnoses subclinical acute rejection |
|
| Relations |
| BioSample |
SAMN10118940 |
| SRA |
SRX4734475 |
