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| Status |
Public on Mar 05, 2019 |
| Title |
Identification of nucleic acids that supports protein renaturation |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Many proteins require RNA to remain soluble in cell and tissue lysate. Here we used RNA- and DNA- immunoprecipitation to identify what types of nucleic acids are associated with these proteins after in vitro renaturation.
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| Overall design |
RNAse-aggregated proteins were renatured with pre-fragmented genomic DNA or total RNA. After removal of insoluble (re-aggregated) proteins, the soluble fraction was subjected to immunoprecipitation or membrane capture. Each IP was done twice on different material and include IP with IgG or GFP antibodies as controls for the RNA and the DNA, respectively. Membrane capture were performed twice on biological replicates but only once for the negative control.
RNA-seq on RNA-immunoprecipitated with antibodies to Abeta, neurofilament heavy chain and Tau in lysate from human neurons. Two biological replicates of each IP were analysed, except for Abeta, where only one sample were available. Significantly associated transcripts were identified by comparing read densities in IP-samples to read densities in samples immunoprecipitated with non-specific IgG antibodies.
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| Contributor(s) |
Aarum J, Sheer D, Cabrera CP, Jones TA, Rajendran S, Giovannoni G, Barnes MR, Malaspina A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Denise Sheer |
| E-mail(s) |
d.sheer@qmul.ac.uk
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| Phone |
+442078822595
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| Organization name |
Barts & The London School of Medicine & Dentistry
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| Department |
Neuroscience & Trauma
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| Street address |
Blizard Institute, 4 Newark Street
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| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA387387 |
| SRA |
SRP107730 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99127_Peaks_DNA_4G8_IP-vs-IgG_IP.txt.gz |
152.9 Kb |
(ftp)(http) |
TXT |
| GSE99127_Peaks_DNA_Mem_pos-vs-Mem_neg.txt.gz |
5.9 Kb |
(ftp)(http) |
TXT |
| GSE99127_Peaks_RNA_4G8_IP-vs-GFP_IP.txt.gz |
198.0 Kb |
(ftp)(http) |
TXT |
| GSE99127_Peaks_RNA_NF-H_IP-vs-GFP_IP.txt.gz |
244.3 Kb |
(ftp)(http) |
TXT |
| GSE99127_Peaks_RNA_tau_IP-vs-GFP_IP.txt.gz |
254.6 Kb |
(ftp)(http) |
TXT |
| GSE99127_Transcripts_IP_4G8_vs_IgG.xlsx |
401.5 Kb |
(ftp)(http) |
XLSX |
| GSE99127_Transcripts_IP_NF-H_vs_IgG.xlsx |
457.6 Kb |
(ftp)(http) |
XLSX |
| GSE99127_Transcripts_IP_tau_vs_IgG.xlsx |
552.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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