RNA-Seq Analysis to investigate the impact of hypoxia on the host responses to Nontypeable Haemophilus influenzae infection in the human explanted lung
RNA-seq (gene expression) · human · 20 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 20 samples: 20 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE280966_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1181561 and SRA study SRP542849. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 10 samples read as cases, 10 as controls.
How we read this: Read from 20 sample titles: 20 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8608123 TL1667, Normoxia, Control
- GSM8608124 TL1667, Normoxia, Infected
- GSM8608125 TL1667, Hypoxia, Control
- GSM8608126 TL1667, Hypoxia, Infected
- GSM8608127 TL2052 ,Normoxia, Control
- GSM8608128 TL2052 ,Normoxia, Infected
- GSM8608129 TL2052, Hypoxia, Control
- GSM8608130 TL2052 ,Hypoxia, Infected
- GSM8608131 TL2054 ,Normoxia, Control
- GSM8608132 TL2054 ,Normoxia, Infected
- GSM8608133 TL2054 ,Hypoxia, Control
- GSM8608134 TL2054 ,Hypoxia, Infected
- GSM8608135 TL2058 ,Normoxia, Control
- GSM8608136 TL2058 ,Normoxia, Infected
- GSM8608137 TL2058 ,Hypoxia, Control
- GSM8608138 TL2058 ,Hypoxia, Infected
- GSM8608139 TL2067 ,Normoxia, Control
- GSM8608140 TL2067 ,Normoxia, Infected
- GSM8608141 TL2067 ,Hypoxia, Control
- GSM8608142 TL2067 ,Hypoxia, Infected
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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.