 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 31, 2018 |
| Title |
Human embryonic stem cell, chimpanzee induced pluripotent stem cell, orangutan induced pluripotent stem cell, rhesus embryonic stem cell, and their derived cortical organoid RNA-seq |
| Organisms |
Macaca mulatta; Pan troglodytes; Pongo abelii; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We compared a 5 week time course of cortical organoid differentiation across human, chimpanzee, orangutan, and rhesus using bulk RNAseq. In addition, single cell RNAseq was performed on a subset of time points from human cells in weeks 0, 1, 2, and 5.
|
| |
|
| Overall design |
Bulk RNAseq of hESCs, ch-iPSCs, or-iPSCs, rhESCs, and each of 6 time points corresponding to weeks 0, 1, 2, 3, 4, and 5 during cortical organoid differentiation. Single cell RNAseq of human ESCs, week 1, week 2, and week 5 organoids.
|
| |
|
| Contributor(s) |
Field AR, Jacobs FM, Fiddes IT, Phillips AP, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V, Rosenkrantz JL, Hauessler M, Katzman S, Salama SR, Haussler D |
| Citation(s) |
29856954, 30639214, 33319914 |
| |
| Submission date |
Oct 26, 2017 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Andrew Ryan Field |
| E-mail(s) |
andrew_field@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
BCMP
|
| Lab |
Adelman
|
| Street address |
45 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (5)
|
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL14954 |
Illumina HiSeq 2000 (Macaca mulatta) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL23423 |
Illumina HiSeq 4000 (Pan troglodytes) |
| GPL24195 |
Illumina HiSeq 4000 (Pongo abelii) |
|
| Samples (55)
|
|
| Relations |
| BioProject |
PRJNA415990 |
| SRA |
SRP121791 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106245_GEO_ReadMe.txt.gz |
439 b |
(ftp)(http) |
TXT |
| GSE106245_RAW.tar |
148.0 Mb |
(http)(custom) |
TAR (of TAR) |
| GSE106245_deseq_baseMean_allF2.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE106245_hg19.RSEM.gene_expression.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
| GSE106245_hg19.cufflinks.filtered.gtf.gz |
51.9 Mb |
(ftp)(http) |
GTF |
| GSE106245_hg19.fantom.lv3.filtered.gtf.gz |
35.0 Mb |
(ftp)(http) |
GTF |
| GSE106245_panTro4.RSEM.gene_expression.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
| GSE106245_panTro4.cufflinks.filtered.gtf.gz |
38.7 Mb |
(ftp)(http) |
GTF |
| GSE106245_panTro4.fantom.lv3.transmap.filtered.gtf.gz |
31.3 Mb |
(ftp)(http) |
GTF |
| GSE106245_ponAbe2.RSEM.gene_expression.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
| GSE106245_ponAbe2.cufflinks.filtered.gtf.gz |
36.7 Mb |
(ftp)(http) |
GTF |
| GSE106245_ponAbe2.fantom.lv3.transmap.filtered.gtf.gz |
30.6 Mb |
(ftp)(http) |
GTF |
| GSE106245_rheMac8.RSEM.gene_expression.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
| GSE106245_rheMac8.cufflinks.filtered.gtf.gz |
37.4 Mb |
(ftp)(http) |
GTF |
| GSE106245_rheMac8.fantom.lv3.transmap.filtered.gtf.gz |
32.2 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...