|
| Status |
Public on Sep 13, 2016 |
| Title |
03-1-0026-1 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
time of blood draw: 1 week post-transplant
race: Caucasian / White
ethnicity: Non-Hispanic/Non-Latino
gender: M
primary disease: Nephritis,@2 other drugs
transplanted organ: Kidney
transplant type: kidney
age at transplant: 55.37
|
| Treatment protocol |
Blood was collected into BD Vacutainer EDTA coated tubes. RNA was isolated from approximately 12 mLs of whole blood PBMCs using the Qiagen QIAamp RNA Blood Mini kit (Germantown, MD) within 2 hours of blood draw.
|
| Growth protocol |
Adults receiving living donor kidney allografts were studied. Patients received thymoglobulin induction and maintenance therapy with tacrolimus or cyclosporine, with mycophenolate and short course steroids to days 5–7 post-transplant. Four of the patients received tacrolimus or cyclosporine prior to transplantation. Five patients were receiving steroids and 9 were receiving mycophenolate at baseline for underlying disease. The subjects had no rejection or any previous rejection at time of each sample collection. Sequential whole blood samples for isolation of PBMCs were collected at baseline (pre-transplant, n = 32), week 1 (n = 31), month 3 (n = 18) and month 6 (n = 15) post-transplant. Some samples were not obtained because patients did not return to the transplant clinic for follow-up center visits and clinical follow ups were performed by referring physician. All patients in this study provided written informed consent following protocol that was approved by the institutional review board of the University of Minnesota.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen QIAamp RNA Blood Mini kit (Germantown, MD)
RNA was quantitated with a Nanodrop 800 spectrophotometer. One μg of each RNA sample was used to prepare RNAseq libraries based on the method as outlined by Zhong and colleagues [reference 17 in published manuscript] with modifications and added quality checks. Sample quantity and integrity was checked using RiboGreen analysis and an Agilent 2100 Bioanalyzer or Caliper equivalent. Each sample passing quality control (RNA mass > 1 μg and RNA Integrity Number > 6) was used to create a polyA+ stranded barcoded RNAseq library using standard protocols. Five samples were pooled for each lane for Illumina Hi-seq 2000 sequencing to generate 20–40 million mapped paired-end reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Native files converted to FASTQ by Minnesota Supercomputing Institute
FASTQ files assessed for quality by FastQC:Read QC
Paired-end reads aligned to human genome (GRCH37/hg19) via Tophat2 using iGenome UCSC reference annontation
Transcript assembly and abundance was determined using Cufflinks with hg_19_genes_2012-30-09.gtf reference annotation
Genome_build: GRCH37/hg19
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Casey Dorr |
| E-mail(s) |
cdorr@mmrf.org
|
| Organization name |
Minneapolis Medical Research Foundation
|
| Street address |
701 Park Avenue
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55415 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE86884 |
Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients |
|
| Relations |
| Reanalyzed by |
GSE122515 |
| BioSample |
SAMN05770098 |
| SRA |
SRX2162322 |
