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Transcriptional profiling of sorted THP1 cells infected with wild-type Mtb (H37Rv) or ESX-1-mutant Mtb

GSE280005 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2024/12/20 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 32 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
32 samples: 16 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
THP1 cells were infected with wild-type or ESX-1-mutant Mtb expressing GFP. Cells were then sorted into infected and bystander populations, and RNAseq was performed.
This dataset
Open GSE280005 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE280005_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1175726 and SRA study SRP540006. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 conditions, mostly in duplicate
THP1, H37Rv infected, 2h_sorted, ×2 THP1, H37Rv Uninfected, 2h_sorted, ×2 THP1, ∆EccCa1-Rv infected, 2h_sorted, ×2 THP1, ∆EccCa1-Rv Uninfected, 2h_sorted, ×2 THP1, H37Rv infected, 4h_sorted, ×2 THP1, H37Rv Uninfected, 4h_sorted, ×2 THP1, ∆EccCa1-Rv infected, 4h_sorted, ×2 THP1, ∆EccCa1-Rv Uninfected, 4h_sorted, ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 of them. 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.

Samples in this study
Datasets on a similar topic

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