|
| Status |
Public on Oct 22, 2015 |
| Title |
Myocyte-RBFox2-nulcear-CLIPseq |
| Sample type |
SRA |
| |
|
| Source name |
cardiac myocytes from WT mouse hearts
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Black Swiss
genotype/variation: wild type
age: 9 weeks
tissue: heart
cell type: cardiac myocytes
chip antibody: anti-RBFox2
chip antibody vendor: Bethyl
chip antibody cat. #: A300-864A
molecule subtype: nuclear RNA
|
| Treatment protocol |
Isolated cardiac myocytes were UV-irradiated at 400mj
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated cardiac myocytes were used to prepare nuclei as described (Widnell et al., 1967). CLIP-seq library was prepared according to previously published standard protocol (Yeo et al., 2009).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CLIP-seq
|
| Data processing |
Sequencing reads were trimmed by using cutadapt program (version 1.2.1). Trimmed reads smaller than 16 nt were discarded.
Reads were mapped to the mouse genome by using Bowtie (version 0.12.7), with parameters "--best --strata -l25 -n2'. Only uniquely mapped reads were kept.
For ChIP-seq, the reads mapped to the same location were kept up to 4. The heart RBFox2 and input ChIP reads were trimmed 3 bp at 5'-end before mapping because of low sequencing qualities. The genomic coverage signal were counted from reads on both strands and normalized to 1 million total reads. The normalized signal from input samples were subtracted from those corresponding IPed samples and negative values were reset as 0.
For Gro-seq, the replicated samples were combined together. The genomic coverage signal were counted in forward and reverse strands separately and normalized to 1 million total reads.
For CLIP-seq, the reads mapped to the same location with same random barcode sequence (attached to read name) were kept to 1. The genomic coverage signal were counted in forward and reverse strands separately, and then normalized to 1 million total reads.
For 3'-end RNA-seq, the reads mapped to the same location were kept up to 4, and only reads in exons were counted. The counts for different samples were normalized to 10 million total reads.
For RASL-seq, the reads were mapped to targetd exon-exon junctions with up to two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files are genomic signals for ChIP-seq, Gro-seq and CLIP-seq samples. The Excel file for RASL-seq samples are counts for targeted isoforms. The Excel file for 3'-end RNA-seq samples are normalized abundance measurements.
|
| |
|
| Submission date |
May 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiang-Dong Fu |
| Organization name |
UC San Diego
|
| Department |
CMM
|
| Lab |
George Palade Laboratories
|
| Street address |
9500 Gilman Drive, Room 231
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0651 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE57926 |
RBFox2 regulates a broad RNA program and is required for genome-wide targeting of polycomb complex |
|
| Relations |
| BioSample |
SAMN02798522 |
| SRA |
SRX551559 |
| Named Annotation |
GSM1397538_Myocyte-RBFox2-nulcear-CLIPseq_r.bw |
| Named Annotation |
GSM1397538_Myocyte-RBFox2-nulcear-CLIPseq_f.bw |
