GEO series

Stem Cell-derived Microglia Exhibit HAND Gene Expression Signature Early Upon Infection with HIV-1 [MDM]

GSE248996 Homo sapiens (human) RNA-seq (gene expression) 23 samples Submitted 2024/05/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 23 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: 23 samples: 7 conditions, mostly in triplicateGroups 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)

HIV-associated neurocognitive disorders (HAND) persist as a notable cause of illness among individuals with HIV. Despite significant progress in antiretroviral therapy (ART), HAND continues to be a major concern, impacting approximately one-third of those infected with HIV. Recent research underscores the pivotal role of microglia, the primary immune cells in the central nervous system (CNS), in the development and progression of HAND.

Read the full summary ↓

The infection and activation of microglia by HIV leads to the release of pro-inflammatory markers, cytokines, chemokines, secondary messengers, and reactive oxygen species (ROS). These factors collectively initiate signalling pathways that contribute to neuroinflammation, a central process in the development of HAND. In order to validate stem cell-derived microglia (iMGL) as a viable model system for HAND investigation, we infected iMGLs and human monocyte-derived macrophages (MDMs) with the primary HIV-1 isolate Ba-L at an MOI of 0.25. Total RNA was extracted from cell populations on days 1, 2, 4, 6, and 8 following infection. Subsequently, we conducted bulk RNA sequencing to examine the longitudinal transcriptomic alterations induced by the virus over this time frame

This dataset

Open GSE248996 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 GSE248996_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 PRJNA1046559 and SRA study SRP474971. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 conditions, mostly in triplicate

MDM_Uninfected_d ×5 MDM_HIV_BaL_d0_biol ×3 MDM_HIV_BaL_d1_biol ×3 MDM_HIV_BaL_d2_biol ×3 MDM_HIV_BaL_d4_biol ×3 MDM_HIV_BaL_d6_biol ×3 MDM_HIV_BaL_d8_biol ×3

Supports a between-group comparison across 23 samples.

How we read this: 7 replicated groups read from 23 sample titles; they account for 23 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

GSM7924403 MDM_Uninfected_d1 MDM_Uninfected_d
GSM7924404 MDM_Uninfected_d2 MDM_Uninfected_d
GSM7924405 MDM_Uninfected_d4 MDM_Uninfected_d
GSM7924406 MDM_Uninfected_d6 MDM_Uninfected_d
GSM7924407 MDM_Uninfected_d8 MDM_Uninfected_d
GSM7924408 MDM_HIV_BaL_d0_biol_rep1 MDM_HIV_BaL_d0_biol
GSM7924409 MDM_HIV_BaL_d0_biol_rep2 MDM_HIV_BaL_d0_biol
GSM7924410 MDM_HIV_BaL_d0_biol_rep3 MDM_HIV_BaL_d0_biol
GSM7924411 MDM_HIV_BaL_d1_biol_rep1 MDM_HIV_BaL_d1_biol
GSM7924412 MDM_HIV_BaL_d1_biol_rep2 MDM_HIV_BaL_d1_biol
GSM7924413 MDM_HIV_BaL_d1_biol_rep3 MDM_HIV_BaL_d1_biol
GSM7924414 MDM_HIV_BaL_d2_biol_rep1 MDM_HIV_BaL_d2_biol
GSM7924415 MDM_HIV_BaL_d2_biol_rep2 MDM_HIV_BaL_d2_biol
GSM7924416 MDM_HIV_BaL_d2_biol_rep3 MDM_HIV_BaL_d2_biol
GSM7924417 MDM_HIV_BaL_d4_biol_rep1 MDM_HIV_BaL_d4_biol
GSM7924418 MDM_HIV_BaL_d4_biol_rep2 MDM_HIV_BaL_d4_biol
GSM7924419 MDM_HIV_BaL_d4_biol_rep3 MDM_HIV_BaL_d4_biol
GSM7924420 MDM_HIV_BaL_d6_biol_rep1 MDM_HIV_BaL_d6_biol
GSM7924421 MDM_HIV_BaL_d6_biol_rep2 MDM_HIV_BaL_d6_biol
GSM7924422 MDM_HIV_BaL_d6_biol_rep3 MDM_HIV_BaL_d6_biol
GSM7924423 MDM_HIV_BaL_d8_biol_rep1 MDM_HIV_BaL_d8_biol
GSM7924424 MDM_HIV_BaL_d8_biol_rep2 MDM_HIV_BaL_d8_biol
GSM7924425 MDM_HIV_BaL_d8_biol_rep3 MDM_HIV_BaL_d8_biol

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GSE248997 Stem Cell-derived Microglia Exhibit HAND Gene Expression Signature Early Upon Infection with HIV-1 [iPSCMG] 23 samples shares hiv-1, hand, cell-derived, microglia, signature, exhibit, early
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GSE293391 Healthy human induced pluripotent stem cell-derived cardiomyocytes exhibit sex dimorphism even without the addition of hormones 18 samples shares cell-derived, exhibit
GSE249992 Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity 17 samples shares cell-derived, signature
GSE249991 Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [Bulk RNA-seq] 16 samples shares cell-derived, signature

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