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| Status |
Public on Jun 20, 2020 |
| Title |
Altered activity-dependent nascent transcription in Rai1-knockdown mature mouse cortical cultures |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We performed the nascent RNA-seq technique, Bru-Seq, and chromatin immunoprecipitation sequencing (ChIP-seq) for Retinoic acid induced 1 (RAI1) using a custom antibody, on mouse neuronal cultures treated with control or Rai1-targeted shRNA, with 4 hour treatment of vehicle, tetrodoxin (TTX) or bicuculline (BIC) and 20 minute labeling of bromouridine.
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| Overall design |
2-3 biological replicates, each consisting of cortices and hippocampi pooled from sex-ratio matched groups of E18 mouse embryos. Cells were plated and cultured for 14 days in Neurobasal + B27 medium, at which point lentiviral delivery of control or Rai1-targeted shRNA was performed. 3 days later, cells were treated with TTX, Bicuculline, or vehicle (water) for 4 hours.
For Bru-seq: In the last 20 minutes, bromouridine was applied to the cells to label nascent RNA. Follow RNA purification, bromouridine-immunoprecipitation was performed to isolate nascent RNAs, preceding cDNA library synthesis. Pooled stranded libraries were run on Illumina Hiseq, single-end, 50 bp reads.
For RAI1 ChIP-seq: Cells were harvested, fixed, and RAI1-bound chromatin isolated. Pooled libraries were run on Illumina NextSeq, single-end, 75 bp reads.
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| Contributor(s) |
Garay PM, Iwase S |
| Citation(s) |
32783930 |
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| Submission date |
Oct 24, 2018 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Patricia Garay |
| E-mail(s) |
pmgaray@umich.edu, patriciamgaray@gmail.com
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| Phone |
7346478811
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| Organization name |
University of Michigan
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| Street address |
1137 Catherine St 5815 Med Sci II
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA498308 |
| SRA |
SRP166779 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE121749_DESeq2_RPKM_FullGeneLength_All_Conditions.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shCtrl_BIC_vs_shCtrl_Veh.txt.gz |
737.0 Kb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shCtrl_TTX_vs_shCtrl_Veh.txt.gz |
733.9 Kb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shRai1_BIC_vs_shCtrl_BIC.txt.gz |
711.2 Kb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shRai1_BIC_vs_shRai1_Veh.txt.gz |
740.4 Kb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shRai1_TTX_vs_shCtrl_TTX.txt.gz |
705.0 Kb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shRai1_TTX_vs_shRai1_Veh.txt.gz |
731.2 Kb |
(ftp)(http) |
TXT |
| GSE121749_DESeq2_shRai1_Veh_vs_shCtrl_Veh.txt.gz |
592.9 Kb |
(ftp)(http) |
TXT |
| GSE121749_Merged_Input_bw1_mm9_norm.bw |
669.6 Mb |
(ftp)(http) |
BW |
| GSE121749_RAW.tar |
3.0 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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