 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 11, 2024 |
| Title |
adult forebrain, genome-wide, rep7 |
| Sample type |
SRA |
| |
|
| Source name |
forebrain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: forebrain
strain: C57BL/6
|
| Treatment protocol |
The mouse line with conditional tAgo2 expression in excitatory neurons was generated by crossing B6Tg(Camk2a-Cre/ERT2) (Erdmann et al. 2007), and B6.Cg-Gt(ROSA)26Sortm1(CAG-GFP/Eif2c2)Zjh/J (Jackson Laboratory #017626). Tamoxifen (2 mg) was administered to mice intraperitoneally once per day for 5 days. Gene induction was allowed to occur for 14-21 days after the final injection before tissue harvest at 10-12 weeks of age.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brain tissue in Homogenization buffer (1X HBSS supplemented with 5 mM MgCl2, 10 mM HEPES (pH 7.4) and 1X HALT protease/phosphatase inhibitor) is homogenized by 12 passes through a 21G needle. UV irradiate homogenates 3x with (4000 µJ/cm2 x 100) on a perfluoroalkoxy (PFA) petri dish, mixing samples between rounds. Transfer irradiated tissue homogenate to a microfuge tube and centrifuge 900 x g for 5 minutes at 4 °C. Immunoprecipitation from the cell pellets were done with anti-Ago2 (2D4, Wako, 018-22021) for total CIMERA-seq, anti-myc (9B11, Cell Signaling, 2276) for cell-selective CIMERA-seq, and anti-IgG1 (Invitrogen, 14-4714-82) for negative control.
Libraries were prepared by intermolecular ligation of small non-coding RNA and target RNA, RNA isolation from Ago protein, ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection.
custom sequencing libraries with 150 base-pair paired-end sequencing and a read depth of 61 – 138 million reads per sample (Illumina HiSeq X or NovaSeq)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Rep7
Forebrain_CIMERA-seq_sample_5-7_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.txt
Forebrain_CIMERA-seq_sample_5-7_peaks.bed.mouse.annotation.txt
|
| Data processing |
Sequencing data were processed using SCRAP (SCRAP release 2.0) bioinformatic pipeline to identify the significant sncRNA:targetRNA interactions in each sample (Eadara et al. 2023; Mills et al. 2022), for which code is deposited at https://github.com/Meffert-Lab/SCRAP.
Peak calling was performed by setting SCRAP variables to consider only high confidence sncRNA binding sites across the genome supported by at least 3 chimeric sncRNA:target RNA reads in at least 2 sample libraries. Peak calling was performed as groups: group1: Forebrain CIEMRA-seq sample 1-4 group 2: Forebrain CIMERA-seq sample 5-7 group 3: Excitatory neuron selective CIMERA-seq sample 1-3 group 4: IgG CIMERA-seq sample 1-2
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include counts for each chimeric RNA (sncRNA:target RNA pairs)
Library strategy: CIMERA-seq
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
Jul 11, 2024 |
| Contact name |
Mollie Meffert |
| Organization name |
Johns Hopkins University School of Medicine
|
| Street address |
725 N. Wolfe St.
|
| City |
Baltimore |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE263988 |
Genome-wide and Cell-type Selective Profiling of In Vivo Small Noncoding RNA:Target RNA Interactions by Chimeric RNA Sequencing |
|
| Relations |
| BioSample |
SAMN40972841 |
| SRA |
SRX24260850 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
