|
| Status |
Public on Feb 05, 2019 |
| Title |
BRN_WT_input_A |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Norad+/+
strain, sex: C57BL/6, female
age: 3 months
|
| Treatment protocol |
Fresh brain samples were first minced in ice-cold PBS and then UV crosslinked at 254nm. Two mice per genotpye were used as biological replicates (A and B).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following immunoprecipitation of PUM2, interacting RNAs were isolated from input and IP samples according to a previously published protocol (Van Nostrand et al. 2016).
Sequencing libraries were similarly prepared as previously described (Van Nostrand et al. 2016). Single-read sequencing was performed on a NextSeq500 platform using a NextSeq 500/550 High Output v2 Kit (Illumina).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PUM2_CLIP_clusters_WT.txt
|
| Data processing |
Adapters were trimmed using Cutadapt with an e-value set to 0.1.
All reads with a length of at least 18 nt were first aligned to Norad and then to GRCm38 (mm10) using Tophat2 (v2.0.12) with default settings.
Only uniquely mapped reads were retained. PCR duplicates were removed based on the information obtained from the unique molecular identifiers.
The read counts of each IP/input pair were obtained for every bin, requiring at least a 50% sequence overlap. The fold-changes for each IP/input pair were calculated. Bins with fold-changes greater than or equal to 4 were considered as clusters.
Finally, clusters were filtered for those that were detected in both biological replicates of either genotype. Clusters that overlapped with at least 30% of their length were merged.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files including genomic location, cluster ID, gene ID and annotation type.
|
| |
|
| Submission date |
Oct 23, 2018 |
| Last update date |
Feb 05, 2019 |
| Contact name |
Joshua Mendell |
| E-mail(s) |
joshua.mendell@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Molecular Biology
|
| Street address |
6000 Harry Hines Blvd., NA6.200A
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE121684 |
Identification of RNAs bound to PUM2 in Norad+/+ and Norad-/- brains [CLIP-seq] |
|
| Relations |
| BioSample |
SAMN10281966 |
| SRA |
SRX4925231 |
