 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 28, 2024 |
| Title |
N6_Day_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole Blood
patientid: N6
group: Day_1
rnaconcentration_ngul: 240.8551
total_rna_ngul: 16859.857
rna_volume_ul: 70
rin: 9.3
isolation_date: 2019-01-01
isolation_personnel: Tsin
time_point: Day_1
age_years: 62
gender: female
ancestry: Caucasian
collection_date: 2017-07-10
neut_range_pre_max_10^6/ml: 1.9 - 9.8
maxfold_increase_neuts: 5.1
imm_neuts_freq_range_pre_max_10^6/ml: 1.0 - 22.6
free_plasma_dna_ng/ml: 297 - 615
collection_date2: 2017-07-10
year_batch: FALSE
cell.free.dna_ng/ml: 5.97579237771369
crp_mg/l: 12.1834379710866
lymphocyte.counts_10^6/ml: -0.127833371509885
monocyte.counts_10^6/ml: -0.544727175441672
neutrophil.cd11b.mfi: 7.26389007706836
neutrophil.cd18.mfi: 6.80239476332431
neutrophil.cd35.mfi: 6.80128303447162
neutrophil.cd62l.mfi: 7.83161727635261
neutrophil.cd63.mfi: 7.46908388492123
neutrophil.cd64.mfi: 7.27100853828099
neutrophil.cd66b.mfi: 8.35983738064003
neutrophil.counts: 2.28238238567653
neutrophil.cxcl1.mfi: 9.05998249038762
neutrophil.cxcl2.mfi: 5.73009978297357
neutrophil.cxcl4.mfi: 8.31434234336979
plasma.cox.2_copies/ul: 6.22937847732564
plasma.dloop_copies/ul: 6.53135856162132
plasma.gapdh_copies/ul: 5.93571396533666
plasma.nd1_copies/ul: 1.69927861643389
platelet.counts_10^6/ml: 3.43398720448515
wbc_10^6/ml: 2.44147709186066
weight._kg: 94
height_m: 1.58
bmi: 37.6542220797949
body.surface.area_m^2: 1.95
ischaemic.heart.disease: 0
smoking: 2
hypertension: 1
hypercholesterolaemia: 0
diabetes: 1
left.ventricular.function: 1
peripheral.vascular.disease: 0
number.of.diseased.coronaries: 3
procedure: CAGS
pre.op.heparin: 2
number.of.grafts: 4
cross.clamp.duration._min: 90
cardiopulmonary.bypass.time._min: 112
circulatory.cardiac.arrest.during.surgery: 0
txa: 1.5
ddavp: 0
new.atrial.fibrilation: 0
stroke: 0
cardiac.arrest: 0
noradrenaline_mg/ml: 3 to9
returned.to.theatre: 0
pneumonia: 0
wound.infection: 0
icu.stay_days: 22
hospital.stay_days: 9
patientid_f: N6
batch: batch1
sirs_days: 2
sirs_score_mean: 1.25
sirs_score_max: 2
sirs: TRUE
sirs_days_group: SIRS_days 2
sirs_score_mean_group: SIRS_score_1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood total RNA was extracted using the PAXgene blood RNA extraction kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. Extracted RNA samples were quality checked using the Agilent 2100 Bioanalyzer platform (Agilent Technologies, Santa Clara, USA).
cDNA libraries were prepared for sequencing using strand specific TrueSeq kits, with ribosomal RNA and globin mRNA depletion. At least 30 million 150 bp paired-end reads were generated per sample using Illumina NovaSeq 6000 (Illumina, San Diego, USA), employing standard protocols at the Victoria Clinical Genetics Services facility (Melbourne, Australia).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Images were analysed in real time by the NovaSeq Control Software v1.6.0 and Real Time Analysis 3 (RTA3) software v3.4.4. RTA performs real-time base calling on the NovaSeq instrument. The Illumina bcl2fastq 2.20.0.422 pipeline was then used to generate sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using Star (v2.6.1) with default parameters, except for the quantMode TranscriptomeSAM setting
Reads were summarised at the gene level using the featureCounts tool from the Subread package (v1.6.4), in a strand-specific manner.
Differential expression was analysed using limma (v3.40.6) from the bioconductor package, following a limma-voom RNASeq123 published workflow
Assembly: GRCh38.p12
Supplementary files format and content: CSV, raw counts
Supplementary files format and content: CSV, normalized counts log2 FPKM
|
| |
|
| Submission date |
Jan 20, 2024 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Katherine R. Martin |
| E-mail(s) |
martin.k@wehi.edu.au
|
| Organization name |
WEHI
|
| Department |
John T. Reid Trusts Laboratory
|
| Street address |
1G Royal Parade!
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE253782 |
Whole blood transcriptomics reveals G-CSF as a mediator of cardiopulmonary bypass- induced systemic inflammatory response syndrome |
|
| Relations |
| BioSample |
SAMN39605419 |
| SRA |
SRX23336021 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
