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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 04, 2010 |
| Title |
Dynamic transcriptomes during neural differentiation of human embryonic stem cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short long, and paired-end sequencing
In order to examine the fundamental mechanisms governing neural differentiation, we analyzed the transcriptome changes that occur during the differentiation of human embryonic stem cells (hESCs) into the neural lineage. Undifferentiated hESCs as well as cells at three stages of early neural differentiation, N1 (early initiation), N2 (neural progenitor), and N3 (early glial-like) were analyzed using a combination of single read, paired-end read, and long read RNA sequencing. The results revealed enormous complexity in gene transcription and splicing dynamics during neural cell differentiation. We found previously unannotated transcripts and spliced isoforms specific for each stage of differentiation. Interestingly, splicing isoform diversity is highest in undifferentiated hESCs and decreases upon differentiation, a phenomenon we call “isoform specialization.” During neural differentiation, we observed differential expression of many types of genes including those involved in key signaling pathways, and a large number of extracellular receptors exhibit stage-specific regulation. These results provide a valuable resource for studying neural differentiation and reveal insights into the mechanisms underlying in vitro neural differentiation of hESCs, such as neural fate specification, NPC identity maintenance and the transition from a predominantly neuronal state into one with increased gliogenic potential
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| Overall design |
Characterization of changes in the transcriptome profiles during early stages of human neural differentiation from H1 !Series_overall_design=hESCs.
454 SFF files are missing.
hESC_B_s9.fastq--> SRR037192
hESC_B_s8.fastq--> SRR037191
hESC_B_s7.fastq--> SRR037190
hESC_B_s6.fastq--> SRR037189
hESC_B_s5.fastq--> SRR037188
hESC_B_s4.fastq--> SRR037187
hESC_B_s3.fastq--> SRR037186
hESC_B_s2.fastq--> SRR037185
hESC_B_s16.fastq--> SRR037184
hESC_B_s15.fastq--> SRR037183
hESC_B_s14.fastq--> SRR037182
hESC_B_s13.fastq--> SRR037181
hESC_B_s12.fastq--> SRR037180
hESC_B_s11.fastq--> SRR037179
hESC_B_s10.fastq--> SRR037178
hESC_B_s1.fastq--> SRR037177
hESC_B_p6_2.fastq--> SRR037176
hESC_B_p6_1.fastq--> SRR037176
hESC_B_p5_2.fastq--> SRR037175
hESC_B_p5_1.fastq--> SRR037175
hESC_B_p4_2.fastq--> SRR037174
hESC_B_p4_1.fastq--> SRR037174
hESC_B_p3_2.fastq--> SRR037173
hESC_B_p3_1.fastq--> SRR037173
hESC_B_p2_2.fastq--> SRR037172
hESC_B_p2_1.fastq--> SRR037172
hESC_B_p1_2.fastq--> SRR037171
hESC_B_p1_1.fastq--> SRR037171
hESC_A_s3.fastq--> SRR037170
hESC_A_s2.fastq--> SRR037169
hESC_A_s1.fastq--> SRR037168
hESC_A_p3_2.fastq--> SRR037167
hESC_A_p3_1.fastq--> SRR037167
hESC_A_p2_2.fastq--> SRR037166
hESC_A_p2_1.fastq--> SRR037166
hESC_A_p1_2.fastq--> SRR037165
hESC_A_p1_1.fastq--> SRR037165
N3_A_s4.fastq--> SRR037226
N3_A_s3.fastq--> SRR037225
N3_A_s2.fastq--> SRR037224
N3_A_s1.fastq--> SRR037223
N3_A_p3_2.fastq--> SRR037222
N3_A_p3_1.fastq--> SRR037222
N3_A_p2_2.fastq--> SRR037221
N3_A_p2_1.fastq--> SRR037221
N3_A_p1_2.fastq--> SRR037220
N3_A_p1_1.fastq--> SRR037220
N2_B_s8.fastq--> SRR037219
N2_B_s7.fastq--> SRR037218
N2_B_s6.fastq--> SRR037217
N2_B_s5.fastq--> SRR037216
N2_B_s4.fastq--> SRR037215
N2_B_s3.fastq--> SRR037214
N2_B_s2.fastq--> SRR037213
N2_B_s1.fastq--> SRR037212
N2_B_p6_2.fastq--> SRR037211
N2_B_p6_1.fastq--> SRR037211
N2_B_p5_2.fastq--> SRR037210
N2_B_p5_1.fastq--> SRR037210
N2_B_p4_2.fastq--> SRR037209
N2_B_p4_1.fastq--> SRR037209
N2_B_p3_2.fastq--> SRR037208
N2_B_p3_1.fastq--> SRR037208
N2_B_p2_2.fastq--> SRR037207
N2_B_p2_1.fastq--> SRR037207
N2_B_p1_2.fastq--> SRR037206
N2_B_p1_1.fastq--> SRR037206
N2_A_s4.fastq--> SRR037205
N2_A_s3.fastq--> SRR037204
N2_A_s2.fastq--> SRR037203
N2_A_s1.fastq--> SRR037202
N2_A_p3_2.fastq--> SRR037201
N2_A_p3_1.fastq--> SRR037201
N2_A_p2_2.fastq--> SRR037200
N2_A_p2_1.fastq--> SRR037200
N2_A_p1_2.fastq--> SRR037199
N2_A_p1_1.fastq--> SRR037199
N1_A_s3.fastq--> SRR037198
N1_A_s2.fastq--> SRR037197
N1_A_s1.fastq--> SRR037196
N1_A_p3_2.fastq--> SRR037195
N1_A_p3_1.fastq--> SRR037195
N1_A_p2_2.fastq--> SRR037194
N1_A_p2_1.fastq--> SRR037194
N1_A_p1_2.fastq--> SRR037193
N1_A_p1_1.fastq--> SRR037193
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| Contributor(s) |
Wu JQ, Habegger L, Snyder M |
| Citation(s) |
20194744 |
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| Submission date |
Feb 12, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Lukas Habegger |
| E-mail(s) |
lukas.habegger@yale.edu
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| Organization name |
Yale University
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| Street address |
266 Whitney Ave
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
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| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9186 |
454 GS FLX (Homo sapiens) |
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| Samples (8)
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| Relations |
| SRA |
SRP002079 |
| BioProject |
PRJNA125337 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE20301_RAW.tar |
3.7 Gb |
(http)(custom) |
TAR (of FA, WIG) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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