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

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Updated January 19, 2022

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.

Mingyu YangPeking Universityyangmingyucherry@gmail.com
Mingyu Yang (Experimental Scientist)1
Liying Yan (Experimental Scientist)1
1Peking University
Hernandez Karina
Muthuraman Pranav
Parisa Nejad

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/3a694703-3084-4ece-9abe-d935fd5f6748

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_2-cell.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_2-cell.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_4-cell.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_4-cell.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_8-cell.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_8-cell.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_ESC.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_ESC.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_Morluae.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_Morluae.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_PE.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_PE.sort.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_RAW.tar,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_TE.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_TE.sort.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_epi.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_epi.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_oocyte.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_oocyte.bed.tdf,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_zygote.bed.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36552/suppl/GSE36552_zygote.bed.tdf
INSDC Project Accessions:
SRP011546
GEO Series Accessions:
GSE36552

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Atlas

None

Analysis Portals

None

Project Label

HumanPreimplantationEmbryosESCs

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

2 anatomical entities

Organ Part

inner cell mass

Selected Cell Types

2 cell types

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

Smart-seq2

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

MultiSampleSmartSeq2_v2.2.6, SmartSeq2SingleSample_v5.1.5

File Format

5 file formats

Cell Count Estimate

124

Donor Count

4
bai124 file(s)bam124 file(s)fastq.gz124 file(s)loom2 file(s)tar.gz1 file(s)