GEO series

Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq

GSE36552 Homo sapiens (human) Single-cell RNA-seq 124 samples Submitted 2013/08/10 Platform GPL11154

At a glance

Single-cell RNA-seq · human · 124 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 124 samples: 18 conditions, mostly with about 8 replicates eachGroups 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.

Summary (written by the submitters)

Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos, and the embryonic stem cells derived from them, isolate individual cells, prepared single cell cDNAs, and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes.

This dataset

Open GSE36552 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE36552_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA153427 and SRA study SRP011546. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 23934149) ↗

Study design

18 conditions, mostly with about 8 replicates each

hESC passage#10 -Cell# ×26 Late blastocyst #1 -Cell# ×12 Late blastocyst #2 -Cell# ×10 hESC passage#0 -Cell# ×8 8-cell embryo#2 -Cell# ×8 8-cell embryo#3 -Cell# ×8 Morulae #1 -Cell# ×8 Morulae #2 -Cell# ×8 +10 more

Supports a between-group comparison across 124 samples.

How we read this: 18 replicated groups read from 124 sample titles; they account for 124 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.

Samples in this study

GSM896803 Oocyte #1 Oocyte #
GSM896804 Oocyte #2 Oocyte #
GSM896805 Oocyte #3 Oocyte #
GSM896806 Zygote #1 Zygote #
GSM896807 Zygote #2 Zygote #
GSM896808 Zygote #3 Zygote #
GSM896809 2-cell embryo#1 -Cell#1 2-cell embryo#1 -Cell#
GSM896810 2-cell embryo#1 -Cell#2 2-cell embryo#1 -Cell#
GSM896811 2-cell embryo#2 -Cell#1 2-cell embryo#2 -Cell#
GSM896812 2-cell embryo#2 -Cell#2 2-cell embryo#2 -Cell#
GSM896813 2-cell embryo#3 -Cell#1 2-cell embryo#3 -Cell#
GSM896814 2-cell embryo#3 -Cell#2 2-cell embryo#3 -Cell#
GSM896815 hESC passage#0 -Cell#1 hESC passage#0 -Cell#
GSM896816 hESC passage#0 -Cell#2 hESC passage#0 -Cell#
GSM922146 4-cell embryo#1 -Cell#1 4-cell embryo#1 -Cell#
GSM922147 4-cell embryo#1 -Cell#2 4-cell embryo#1 -Cell#
GSM922148 4-cell embryo#1 -Cell#3 4-cell embryo#1 -Cell#
GSM922149 4-cell embryo#1 -Cell#4 4-cell embryo#1 -Cell#
GSM922150 4-cell embryo#2 -Cell#1 4-cell embryo#2 -Cell#
GSM922151 4-cell embryo#2 -Cell#2 4-cell embryo#2 -Cell#
GSM922152 4-cell embryo#2 -Cell#3 4-cell embryo#2 -Cell#
GSM922153 4-cell embryo#2 -Cell#4 4-cell embryo#2 -Cell#
GSM922154 4-cell embryo#3 -Cell#1 4-cell embryo#3 -Cell#
GSM922155 4-cell embryo#3 -Cell#2 4-cell embryo#3 -Cell#
GSM922156 4-cell embryo#3 -Cell#3 4-cell embryo#3 -Cell#
GSM922157 4-cell embryo#3 -Cell#4 4-cell embryo#3 -Cell#
GSM922158 8-cell embryo#1 -Cell#1 8-cell embryo#1 -Cell#
GSM922159 8-cell embryo#1 -Cell#2 8-cell embryo#1 -Cell#
GSM922160 8-cell embryo#1 -Cell#3 8-cell embryo#1 -Cell#
GSM922161 8-cell embryo#1 -Cell#4 8-cell embryo#1 -Cell#
GSM922162 8-cell embryo#2 -Cell#1 8-cell embryo#2 -Cell#
GSM922163 8-cell embryo#2 -Cell#2 8-cell embryo#2 -Cell#
GSM922164 8-cell embryo#2 -Cell#3 8-cell embryo#2 -Cell#
GSM922165 8-cell embryo#2 -Cell#4 8-cell embryo#2 -Cell#
GSM922166 8-cell embryo#2 -Cell#5 8-cell embryo#2 -Cell#
GSM922167 8-cell embryo#2 -Cell#6 8-cell embryo#2 -Cell#
GSM922168 8-cell embryo#2 -Cell#7 8-cell embryo#2 -Cell#
GSM922169 8-cell embryo#2 -Cell#8 8-cell embryo#2 -Cell#
GSM922170 8-cell embryo#3 -Cell#1 8-cell embryo#3 -Cell#
GSM922171 8-cell embryo#3 -Cell#2 8-cell embryo#3 -Cell#

+ 84 more — browse all 124 samples with per-sample file links →

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GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares pluripotency, rna-seq, stem
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