RNA-seq of KDM4A, B and C siRNA knockdown in NB cells
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: 12 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
- Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastomaCell reports. Medicine · 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 GSE207013_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 PRJNA853317 and SRA study SRP383792. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.
- GSM6267988 BE2C_siCtrl2_1 BE2C_siCtrl2
- GSM6267989 BE2C_siCtrl2_2 BE2C_siCtrl2
- GSM6267990 BE2C_siKDM4A36_1 BE2C_siKDM4A36
- GSM6267991 BE2C_siKDM4A36_2 BE2C_siKDM4A36
- GSM6267992 BE2C_siKDM4B_67 BE2C_siKDM4B
- GSM6267993 BE2C_siKDM4B_68 BE2C_siKDM4B
- GSM6267994 BE2C_siKDM4C90_1 BE2C_siKDM4C90
- GSM6267995 BE2C_siKDM4C90_2 BE2C_siKDM4C90
- GSM6267996 KELLY_siCtrl2_1 KELLY_siCtrl2
- GSM6267997 KELLY_siCtrl2_2 KELLY_siCtrl2
- GSM6267998 KELLY_siKDM4A36_1 KELLY_siKDM4A36
- GSM6267999 KELLY_siKDM4A36_2 KELLY_siKDM4A36
- GSM6268000 KELLY_siKDM4B_67 KELLY_siKDM4B
- GSM6268001 KELLY_siKDM4B_68 KELLY_siKDM4B
- GSM6268002 KELLY_siKDM4C90_1 KELLY_siKDM4C90
- GSM6268003 KELLY_siKDM4C90_2 KELLY_siKDM4C90
- GSM6268004 SKNAS_siCtrl2_1 SKNAS_siCtrl2
- GSM6268005 SKNAS_siCtrl2_2 SKNAS_siCtrl2
- GSM6268006 SKNAS_siKDM4A36_1 SKNAS_siKDM4A36
- GSM6268007 SKNAS_siKDM4A36_2 SKNAS_siKDM4A36
- GSM6268008 SKNAS_siKDM4B_67 SKNAS_siKDM4B
- GSM6268009 SKNAS_siKDM4B_68 SKNAS_siKDM4B
- GSM6268010 SKNAS_siKDM4C90_1 SKNAS_siKDM4C90
- GSM6268011 SKNAS_siKDM4C90_2 SKNAS_siKDM4C90
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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.