Mono and biallelic inactivation of Huntingtin gene in patient-specific iPS cells reveal HTT roles in striatal development and in neuronal functions impaired in Huntington’s disease
RNA-seq (gene expression) · human · 31 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
- 31 samples: 31 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
- Mono- and Biallelic Inactivation of Huntingtin Gene in Patient-Specific Induced Pluripotent Stem Cells Reveal HTT Roles in Striatal Development and Neuronal FunctionsJournal of Huntington's disease · 2024
Read the full summary ↓
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 GSE228254_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 PRJNA949142 and SRA study SRP429475. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 31 sample titles: 31 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.
- GSM7117783 IonXpress_011_R_2019_10_11_14_46_22_NGS55_libQ195
- GSM7117784 IonXpress_012_R_2019_10_11_14_46_22_NGS55_libQ196
- GSM7117785 IonXpress_013_R_2019_10_10_17_02_28_NGS56_libQ197
- GSM7117786 IonXpress_014_R_2019_10_10_17_02_28_NGS56_libQ198
- GSM7117787 IonXpress_016_R_2019_10_11_14_46_22_NGS55_libQ200
- GSM7117788 IonXpress_017_R_2019_10_10_17_02_28_NGS56_libQ201
- GSM7117789 IonXpress_018_R_2019_10_10_17_02_28_NGS56_libQ202
- GSM7117790 IonXpress_019_R_2019_10_11_14_46_22_NGS55_libQ203
- GSM7117791 IonXpress_020_R_2019_10_11_14_46_22_NGS55_libQ204
- GSM7117792 IonXpress_021_R_2019_10_10_17_02_28_NGS56_libQ205
- GSM7117793 IonXpress_022_R_2019_10_10_17_02_28_NGS56_libQ206
- GSM7117794 IonXpress_023_R_2019_10_11_14_46_22_NGS55_libQ207
- GSM7117795 IonXpress_024_R_2019_10_11_14_46_22_NGS55_libQ208
- GSM7117796 IonXpress_047_R_2019_10_10_17_02_28_NGS56_libQ209
- GSM7117797 IonXpress_048_R_2019_10_10_17_02_28_NGS56_libQ210
- GSM7117798 IonXpress_008_R_2019_02_26_15_45_33_NGS50_libQ145_ML51b
- GSM7117799 IonXpress_009_R_2019_02_26_15_45_33_NGS50_libQ146_ML51d
- GSM7117800 IonXpress_010_R_2019_02_26_15_45_33_NGS50_libQ147_ML58a
- GSM7117801 IonXpress_011_R_2019_07_19_09_53_20_NGS50_libQ148_ML58b
- GSM7117802 IonXpress_012_R_2019_02_26_15_45_33_NGS50_libQ149_ML50d
- GSM7117803 IonXpress_013_R_2019_02_26_15_45_33_NGS50_libQ150_ML57d
- GSM7117804 IonXpress_014_R_2019_02_26_15_45_33_NGS50_libQ151_ML52
- GSM7117805 IonXpress_015_R_2019_07_19_09_53_20_NGS50_libQ152_ML59c
- GSM7117806 IonXpress_016_R_2019_02_26_15_45_33_NGS50_libQ153_ML53c
- GSM7117807 IonXpress_017_R_2019_02_26_15_45_33_NGS50_libQ154_ML60b
- GSM7117808 IonXpress_018_R_2019_02_26_15_45_33_NGS50_libQ155_ML55
- GSM7117809 IonXpress_019_R_2019_07_19_09_53_20_NGS50_libQ156_ML62b
- GSM7117810 IonXpress_020_R_2019_02_26_15_45_33_NGS50_libQ157_ML54d
- GSM7117811 IonXpress_021_R_2019_02_26_15_45_33_NGS50_libQ158_ML61b
- GSM7117812 IonXpress_022_R_2019_02_26_15_45_33_NGS50_libQ159_ML56
- GSM7117813 IonXpress_023_R_2019_07_19_09_53_20_NGS50_libQ160_ML56d
- GSE306330 RNA-seq of RB1-biallelic inactivation mice and HCC cell lines treated with drug 36 samples shares inactivation, biallelic
- GSE270472 Huntingtin loss-of-function contributes to transcriptional deregulation in Huntington’s disease (RNA-Seq) 11 samples shares huntingtin, huntington
- GSE263212 https://pubmed.ncbi.nlm.nih.gov/42007670/ 6 samples shares htt
- GSE322198 Female iPSC X-chromosome inactivation (XCI) erosion and its transcriptomic effects during CRISPR gene editing and neural differentiation 228 samples shares inactivation
- GSE234607 Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease 112 samples shares inactivation
- GSE221617 Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells 105 samples shares patient-specific
- GSE305337 Patient-Specific Pharmacogenomics demonstrates xCT as Predictive Therapeutic Target in Colon Cancer with Possible Implications in Tumor Connectivity 73 samples shares patient-specific
- GSE240370 Transcriptomic analysis of the in vivo effects of CDK8/19 inactivation in 22Rv1 xenografts growing in intact and castrated NSG mice 66 samples shares inactivation
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.