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| Status |
Public on Sep 18, 2018 |
| Title |
I60-50 |
| Sample type |
SRA |
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| Source name |
hESC-derived cortical GABA interneuron
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC-derived cortical GABA interneuron
foxg1 dosage: 60%
differentiation stage: day 60
asv concentration: 50 nM
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| Treatment protocol |
ASV treatment started from day4.
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| Growth protocol |
hPSCs were cultured until reach ~80 confluences. Induction of neural progenitors was adapted from previous article. On day 0, cells were dissociated with Dispase (1 U ml−1), then hPSCs aggregates were harvested by centrifugation and plated in ultra-low-attachment 10 cm dishes (Corning, 430591) to form embryoid bodies. From day 1, the telencephalic induction was started by changing the medium to NIM medium with dual SMAD inhibition consisting of DMEM-F12, 1x N2 supplement (A1370701), 1x B27 supplement, minus vitamin A (12587010), 1x GlutaMAX Supplement (35050061), 0.5X MEM Non-Essential Amino Acids Solution (11140050), 110 μM 2-mercaptoethanol (Sigma-Aldrich, M6250), 0.05% (v/v) Bovine Albumin Fraction V Solution (Sigma-Aldrich, B2064), 1x Penicillin-Streptomycin (10378016), 100 nM LDN193189 (Selleck, S2618), 10 μM SB431542 (Slleck, S1067), 2 μM XAV939 (Selleck, S1180). Media was replenished daily until day 8. Then, EBs were plated on Matrigel (BD, 356234) pre-coated 6-well plates and neuronal rosettes could be observed within a few days. From day 9, medium was changed to NPC medium consisting of DMEM-F12, 0.15% (w/v) Detrose (Sigma-Aldrich, G6152), 110 μM 2-mercaptoethanol (Sigma-Aldrich, M6250), 1x N2 supplement, 1x B27 supplement without vitamin A, 20 ng/ml FGF2 (Peprotech). NPC medium was changed daily for 4 days until day 13.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 10^6 cells using the miRNeasy Mini Kit (QIAGEN, 217004).
mRNA were purified using poly-T oligo-attached magnetic beads. Then, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The first strand cDNA were produced from cleaved RNA fragments using reverse transcriptase and random primers and then second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were purified and enriched with PCR amplification. Finally, we quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
FOXG1s/s hESC line
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| Data processing |
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.
The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study.
The BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Sep 17, 2018 |
| Last update date |
Sep 18, 2018 |
| Contact name |
Baoyang Hu |
| E-mail(s) |
byhu@ioz.ac.cn
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| Phone |
010-64806297
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| Organization name |
Institute of Zoology
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| Department |
State Key Laboratory of Stem Cell and Reproductive Biology
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| Street address |
Beichenxilu
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| City |
Beijing |
| State/province |
Select State/Province |
| ZIP/Postal code |
100000 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE120079 |
Next-generation sequencing facilitates quantitative analysis of the transcriptomes of FOXG1 100% dosage, FOXG1 60% dosage, FOXG1 30% dosage, and FOXG1 0% dosage GABA interneurons derived from human embryonic stem cells |
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| Relations |
| BioSample |
SAMN10079697 |
| SRA |
SRX4705526 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3392989_I60-50.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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