GEO series
Reprograming human fibroblasts into Sertoli cells: a tool for personalized medicine
GSE246236
Homo sapiens (human)
RNA-seq (gene expression)
41 samples
Submitted 2024/03/01
Platform GPL20301
At a glance
RNA-seq (gene expression) · human · 41 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
- 41 samples: 41 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.
- Paper
- Reprograming skin fibroblasts into Sertoli cells: a patient-specific tool to understand effects of genetic variants on gonadal developmentBiology of sex differences · 2024
Summary (written by the submitters)
Differences of Sex Development (DSD) are a set of conditions where development of chromosomal, gonadal, or anatomical sex is atypical. With overlapping phenotypes and multiple genes involved, poor diagnostic yields are achieved for many of these conditions. The current DSD diagnostic regimen can be augmented by investigating transcriptome/proteome in vivo, but it is hampered by the unavailability of affected gonadal tissue at the relevant developmental stage.
Read the full summary ↓
We try to mitigate this limitation by reprogramming readily available skin tissue-derived dermal fibroblasts into Sertoli cells (SC), which could then be deployed for different diagnostic strategies. SCs form the target cell type of choice because they act like an organizing center of embryonic gonadal development and many DSD arise when these developmental processes go awry. Methods: We employed a computational predictive algorithm for cell conversions called Mogrify to predict the transcription factors (TFs) required for direct reprogramming of human dermal fibroblasts into SCs. We established trans-differentiation culture conditions where stable transgenic expression of these TFs was achieved in 46, XY adult dermal fibroblasts using lentiviral vectors. The resulting Sertoli like cells (SLCs) were validated for SC phenotype using several approaches. Results: SLCs exhibited Sertoli-like morphological and cellular properties as revealed by morphometry and xCelligence cell behavior assays. They also showed Sertoli-specific expression of molecular markers such as SOX9, PTGDS, BMP4, or DMRT1 as revealed by IF imaging, RNAseq and qPCR. The SLC transcriptome shared about two thirds of its differentially expressed genes with a human adult SC transcriptome and expressed markers typical of embryonic SCs. Notably, SLCs lacked expression of most markers of other gonadal cell types such as Leydig, germ, peritubular myoid or granulosa cells. Conclusions: The trans-differentiation method was applied to a variety of commercially available 46, XY fibroblasts derived from patients with DSD and to a 46, XX cell line. The DSD SLCs displayed altered levels of trans-differentiation in comparison to normal 46, XY-derived SLCs, thus showcasing the robustness of this new trans-differentiation model.
Published in
Parivesh A, Délot E, Reyes A et al.
· Biology of sex differences 2024
· PMID 38520033
· doi:10.1186/s13293-024-00599-y
This dataset
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.
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 GSE246236_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1032086 and SRA study SRP468441. Searching any of these in the dataset finder brings you back here.
Study design
41 samples, each with a distinct title — no replicated groups
Supports a case/control comparison: 9 samples read as cases, 25 as controls.
How we read this: Read from 41 sample titles: 41 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.
Samples in this study
- GSM7865360 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 6 transcription factor (TF) treatment [AP37]
- GSM7865361 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 6TF treatment [AP39]
- GSM7865362 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 8TF treatment [AP34]
- GSM7865363 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with 8TF treatment [AP35]
- GSM7865364 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with Green Fluroscent protein (GFPC) [AP31]
- GSM7865365 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with GFPC [AP32]
- GSM7865366 Gonadal fibroblasts from a 1-year-old 46, XY female;SRXY1; with GFPC [AP33]
- GSM7865367 Fibroblasts derived from a 3-week-old male with a WT1 deletion with 6TF treatment [AP50]
- GSM7865368 Fibroblasts derived from a 3-week-old male with a WT1 deletion with 6TF treatment [AP51]
- GSM7865369 Fibroblasts derived from a 3-week-old male with a WT1 deletion with 8TF treatment [AP47]
- GSM7865370 Fibroblasts derived from a 3-week-old male with a WT1 deletion with 8TF treatment [AP48]
- GSM7865371 Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC [AP43]
- GSM7865372 Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC [AP44]
- GSM7865373 Fibroblasts derived from a 3-week-old male with a WT1 deletion with GFPC [AP45]
- GSM7865374 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF [AP22]
- GSM7865375 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF [AP23]
- GSM7865376 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 6TF [AP24]
- GSM7865377 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF [AP19]
- GSM7865378 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF [AP20]
- GSM7865379 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with 8TF [AP21]
- GSM7865380 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC [AP16]
- GSM7865381 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC [AP17]
- GSM7865382 Skin fibroblasts derived from a 25-year-old 46, XX healthy female; with GFPC [AP18]
- GSM7865383 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF [AP61]
- GSM7865384 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF [AP62]
- GSM7865385 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 6TF [AP63]
- GSM7865386 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF [AP58]
- GSM7865387 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF [AP59]
- GSM7865388 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with 8TF [AP60]
- GSM7865389 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC [AP55]
- GSM7865390 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC [AP56]
- GSM7865391 skin fibroblasts derived from a 46,XY patient with campomelic dysplasia;with GFPC [AP57]
- GSM7865392 Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC [AP01]
- GSM7865393 Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC [AP02]
- GSM7865394 Normal human adult 46, XY primary dermal fibroblast (HDFa), with GFPC [AP03]
- GSM7865395 Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF [AP07]
- GSM7865396 Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF [AP08]
- GSM7865397 Normal human adult 46, XY primary dermal fibroblast (HDFa), with 6TF [AP09]
- GSM7865398 Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF [5-a]
- GSM7865399 Normal human adult 46, XY primary dermal fibroblast (HDFa), with 8TF [5-b]
+ 1 more — browse all 41 samples with per-sample file links →
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