 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 16, 2019 |
| Title |
Baseline_patient_4 |
| Sample type |
SRA |
| |
|
| Source name |
Baseline_patient
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: healthy volunteer
treatment: none
tissue: Blood
|
| Treatment protocol |
Metformin was administered to healthy volunteers, 1000mg twice per day
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood samples were stored in PAXgene RNA tubes (Preanalytix) and then total RNA was extracted using the PAXgene blood miRNA kit (Qiagen). Globin transcripts were depleted using GLOBINclear TM (Invitrogen).
TruSeq stranded mRNA library prep kit (Illumina) according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment: STAR, version 2.5.1b
Quantification: HT-seq count, version 0.6.1, f=bam, r=name, s=rev, m=union, i=gene id
Normalization: DESeq2, version 1.12.4
Genome_build: Human_g1k_v37
Supplementary_files_format_and_content: [txt] HT-Seq output, read count for each ensembl gene id, un-normalized, un-filtered
|
| |
|
| Submission date |
Aug 14, 2017 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Jackie Cliff |
| E-mail(s) |
jackie.cliff@lshtm.ac.uk, Jacqueline.cliff@brunel.ac.uk
|
| Organization name |
London School of Hygiene & Tropical Medicine
|
| Department |
Immunology and Infection
|
| Street address |
Keppel Street
|
| City |
London |
| ZIP/Postal code |
WC1E 7HT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE102633 |
Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects [Ex vivo Blood RNA-Seq] |
| GSE102678 |
Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects |
|
| Relations |
| BioSample |
SAMN07503801 |
| SRA |
SRX3092079 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2742063_UCLGNS1189-7.txt.gz |
205.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
