|
| Status |
Public on Mar 01, 2021 |
| Title |
10046_ES-I_8 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 10046_ES-I_8
grouping: ES-I_8
timing: I_8
outcome: survived
treatment: Early
treatment-outcome code: ES
baseline cd4+: 13
baseline lfa (crag): 32000
baseline hiv_rna: 74383
age: 26
read length: 125
|
| Treatment protocol |
see https://clinicaltrials.gov/ct2/show/NCT01075152
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total ribonucleic acid (RNA) was extracted from whole blood using PAXgene Blood RNA kits (QIAGEN Inc.) according to the manufacturer’s protocol, and quantity was measured by RiboGreen RNA Quantification.
The Clontech StrandedRNA Pico Mammalian kit was used for library creation. Paired-end (2x125bp or x50bp) sequencing was done on a HiSeq2500 instrument, for 125 cycles, using v4 chemistry (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Fastq files were processed using the Minnesota Supercomputing Institute Unix interface: the qualities of raw reads were assessed and trimmed (in Trimmomatic), if necessary.
The alignment and mapping of sequencing reads to a reference transcriptome (hg38) was performed with HISAT2 (hierarchical indexing for spliced alignment of transcripts).
Transcript expression was normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and quantified using Cuffquant (Cufflinks workflow). Â
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samoles ...
|
| |
|
| Submission date |
Dec 09, 2020 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Irina Vlasova-St. Louis |
| E-mail(s) |
irinastl@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Medicine
|
| Street address |
2001 6th St SE
|
| City |
Minnespolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE162914 |
Transcriptomic biomarker pathways associated with death in HIV-infected patients with cryptococcal meningitis |
|
| Relations |
| BioSample |
SAMN17037273 |
| SRA |
SRX9656860 |
