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Sample GSM6733211 Query DataSets for GSM6733211
Status Public on Nov 24, 2022
Title Evi5_MO_1
Sample type SRA
 
Source name limb bud
Organism Xenopus laevis
Characteristics tissue: limb bud
genotype: Wild type
treatment: Evi5 morpholino injected
Treatment protocol For limb amputation, animals were anesthetized with 0.02% MS-222, NF stage 52-53 tadpole hindlimbs were amputated with a surgical scissor at the level of presumptive knee, and froglet forelimbs and axolotl hindlimbs were amputated at midulna/radius. Microinjection and electroporation in the tadpoles were performed as described (Zhang et al., 2018b). Briefly, animals of selected stages were anesthetized with 0.02% MS-222 (Sigma-Aldrich) and injected with control or evi5 Mo.
Extracted molecule total RNA
Extraction protocol Tadpole were anesthetized with 0.02% MS-222 and collect 10 limb buds in a group. Total RNA was extracted from the cells using TRIzolĀ® Reagent (Invitrogen) and genomic DNA was removed using DNase I (TaKara)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75). Then clean reads were separately aligned to reference genome with orientation mode using hisat2 (https://ccb.jhu.edu/software/hisat2/index.shtml) software.
Assembly: XENLA_XenBase_GeneNames
Supplementary files format and content: fPKM
 
Submission date Nov 15, 2022
Last update date Nov 24, 2022
Contact name Gufa Lin
E-mail(s) lingufa@tongji.edu.cn
Organization name Tongji University
Department Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University
Street address 1239 Siping road Tongji university
City Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL28901
Series (1)
GSE218034 Evi5 is required for Xenopus limb and tail regeneration
Relations
BioSample SAMN31742536
SRA SRX18275286

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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