Gene expression analysis of human sickle cell disease (SCD) and healthy donor (HD) CD34+ hematopoietic stem/progenitor cells (HSPCs) treated with CRISPR/Cas9 targeting the HBG promoters or untreated samples
RNA-seq (gene expression) · human · 24 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
- 24 samples: 6 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.
- Paper
- Safety and efficacy studies of CRISPR-Cas9 treatment of sickle cell disease highlights disease-specific responsesMolecular therapy : the journal of the American Society of Gene Therapy · 2024
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 GSE248671_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 PRJNA1045560 and SRA study SRP474403. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 24 sample titles; they account for 12 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.
- GSM7918579 HD1_197 HD1
- GSM7918580 HD1_196 HD1
- GSM7918581 HD1_AAVS1
- GSM7918582 HD1_UT
- GSM7918583 HD2_197 HD2
- GSM7918584 HD2_196 HD2
- GSM7918585 HD2_AAVS1
- GSM7918586 HD2_UT
- GSM7918587 HD3_197 HD3
- GSM7918588 HD3_196 HD3
- GSM7918589 HD3_AAVS1
- GSM7918590 HD3_UT
- GSM7918591 SCD1_197 SCD1
- GSM7918592 SCD1_196 SCD1
- GSM7918593 SCD1_AAVS1
- GSM7918594 SCD1_UT
- GSM7918595 SCD2_197 SCD2
- GSM7918596 SCD2_196 SCD2
- GSM7918597 SCD2_AAVS1
- GSM7918598 SCD2_UT
- GSM7918599 SCD3_197 SCD3
- GSM7918600 SCD3_196 SCD3
- GSM7918601 SCD3_AAVS1
- GSM7918602 SCD3_UT
- GSE244257 Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells 83 samples shares crispr, cas9, hematopoietic
- GSE290621 Quadruple adenine base edited allogeneic CAR T cells outperform CRISPR/Cas9 nuclease engineered T cells [RNA-seq] 33 samples shares crispr, cas9
- GSE301632 Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma. 27 samples shares crispr, cas9
- GSE303100 Dissecting Resistance to CDK4/6 Inhibition in Experimental Glioma via Genome-wide CRISPR-Cas9 Screening 24 samples shares crispr, cas9
- GSE240468 Silencing of NFYC-AS1 by Gapmer antisense oligonucleotides and CRISPR/Cas9 TSS deletion. 23 samples shares crispr, cas9
- GSE283554 A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics 22 samples shares crispr, cas9
- GSE226978 RNA-Sequencing Analysis of LNCaP Wildtype (WT) and RB-p53 CRISPR-Cas9 Double Knockout (DKO) Cells Treated with Enzalutamide 16 samples shares crispr, cas9
- GSE319117 Simultaneous orthogonal cell engineering by a single CRISPR-Cas9 polyfunctional editor [RNA-seq T-cells B2M/TET2/TGFBR2] 14 samples shares crispr, cas9
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.