Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 24 samples: 20 distinct titles, 2 of them repeatedGroups 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.
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 GSE299579_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 PRJNA1275004 and SRA study SRP589419. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 4 samples read as cases, 13 as controls.
How we read this: Read from 24 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.
- GSM9022158 Hand1 wildtype E13.5 transverse sections V52L19-052_A1
- GSM9022159 Hand1 wildtype E13.5 transverse sections V52L19-052_B1
- GSM9022160 Hand1 wildtype E13.5 transverse sections V52L18-318_B1
- GSM9022161 Hand1 wildtype E13.5 transverse sections V52L18-318_A1
- GSM9022162 Hand1 wildtype E13.5 transverse sections V52L18-320_A1
- GSM9022163 Hand1 wildtype E13.5 transverse sections V52L18-320_B1
- GSM9022164 Hand1 wildtype E13.5 transverse sections V52L19-023_A1
- GSM9022165 Hand1 wildtype E13.5 transverse sections V52L19-023_B1
- GSM9022166 Hand1^Hand2/Hand2 E13.5 transverse sections V52L19-003_A1
- GSM9022167 Hand1^Hand2/Hand2 E13.5 transverse sections V52L19-003_B1
- GSM9022168 Hand1^Hand2/Hand2 E13.5 transverse sections V52L06-338_A1
- GSM9022169 Hand1^Hand2/Hand2 E13.5 transverse sections V52L06-338_B1
- GSM9022170 Hand1^Hand2/Hand2 E13.5 transverse sections V52L18-371_A1
- GSM9022171 Hand1^Hand2/Hand2 E13.5 transverse sections V52L18-371_B1
- GSM9022172 Hand1^Hand2/Hand2 E13.5 transverse sections V52L19-098_B1
- GSM9036097 E13.5 Hand1 Hand2/Hand2 mutant sample 24-7
- GSM9036098 E13.5 Hand1 Hand2/Hand2 mutant sample LE-6
- GSM9036099 E13.5 Hand1 Hand2/Hand2 mutant sample LE-7
- GSM9036100 E13.5 Hand1 Hand2/Hand2 mutant sample R3-2
- GSM9036101 E13.5 Hand1 wild type sample REFvB-1
- GSM9036102 E13.5 Hand1 wild type sample REFvB-2
- GSM9036103 E13.5 Hand1 wild type sample REFvB-3
- GSM9036104 E13.5 Hand1 wild type sample REFvB-4
- GSM9036105 E13.5 Hand1 wild type sample NE-4
- GSE299253 Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [scRNA-seq] 9 samples shares hand1, hand2, replacement, omphalocele, occurrence, overlap, defects, unique
- GSE223771 Hand1 KO HAND2 replacement RNA-Seq data 11 samples shares hand1, hand2, replacement
- GSE311984 Endocardial HAND2 orchestrates hypoxic and TGFbeta signaling to modulate coronary artery formation 19 samples shares hand2
- GSE278736 HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [RNA-Seq] 12 samples shares hand2
- GSE311981 Endocardial HAND2 orchestrates hypoxic and TGFbeta signaling to modulate coronary artery formation [CUT&Tag] 9 samples shares hand2
- GSE245711 Effect of depletion of Hand1 and Foxf1 on gene expression during CM differentiation of E14 embryonic stem cells II 8 samples shares hand1
- GSE311982 Endocardial HAND2 orchestrates hypoxic and TGFbeta signaling to modulate coronary artery formation [RNA-Seq] 8 samples shares hand2
- GSE299217 HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [ATAC, Cut & Tag] 5 samples shares hand2
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.