Experiment information
Accession CRX048011
Organism Danio rerio
Title RIP_0hpf_rep1_Ybx1-RIP
BioProject PRJCA001013
BioSample SAMC067639
Platform Illumina HiSeq 2500
Library
Library name Construction protocol Strategy Source Selection Layout
500 zebrafish embryos at shield stage (0 hpf) were resuspended with 2 ml lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 0.4 U/?l RNasin) by rotating at 4°C for 30 min and centrifuged at 15,000 g for 15 min. The supernatant was collected and pre-cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 ?l pre-cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti-Ybx1 antibody (prepared by AbMax, China) and 30 ?l Protein A Dynabeads for 4 h at 4°C or overnight. After washing with1 ml ice-cold NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 0.4U/µl RNasin) for eight times and once with 1ml ice-cold 1× PK buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA , 0.2% SDS), the beads was treated in 200 ul PK buffer containing 20 ul proteinase K (Roche, 0311582001) for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 (pH4.3~4.7) and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase (Invitrogen, AM2238). RIP-Seq TRANSCRIPTOMIC PCR PAIRED
Processing Planned read length (bp) for mate 1: 150
Planned read length (bp) for mate 2: 150
Insert size (bp): 240
Release date2019-06-12
Run
Run Accession Release date Run Data File Information
File nameFile size (MB)
CRR053065 2019-06-12 RIP_0hpf_rep1_R1.fastq.gz
RIP_0hpf_rep1_R2.fastq.gz
2,271.41
2,287.01
Submittersun baofa (sunbf@big.ac.cn)
OrganizationsBeijing Institute of Genomics, Chinese Academy of Sciences
Date submitted2019-04-12