Next Generation Sequencing (NGS) Facilitates Quantitative Analysis of Non-silencing Control and EP300 Knockdown Transcriptomes
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × NS1 vs 3 × NS2 vs 3 × EP300 KD1 vs 3 × EP300 KD2Groups 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 GSE114742_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 PRJNA472457 and SRA study SRP148636. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 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.
- GSM3149175 NS1 rep1 NS1
- GSM3149176 NS1 rep2 NS1
- GSM3149177 NS1 rep3 NS1
- GSM3149178 NS2 rep1 NS2
- GSM3149179 NS2 rep2 NS2
- GSM3149180 NS2 rep3 NS2
- GSM3149181 EP300 KD1 rep1 EP300 KD1
- GSM3149182 EP300 KD1 rep2 EP300 KD1
- GSM3149183 EP300 KD1 rep3 EP300 KD1
- GSM3149184 EP300 KD2 rep1 EP300 KD2
- GSM3149185 EP300 KD2 rep2 EP300 KD2
- GSM3149186 EP300 KD2 rep3 EP300 KD2
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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.