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Sample GSM2428226 Query DataSets for GSM2428226
Status Public on Mar 31, 2017
Title Endoderm_Donor_Kdm5wt_3 (Group5)
Sample type SRA
 
Source name Donor endoderm cells expressing Kdm5bwt
Organism Xenopus laevis
Characteristics starting material: single embryo
developmental stage/condition: in vitro fertilized embryo stage 18 expressing Kdm5bwt
cell type: endoderm
pairing of samples: Group5
Growth protocol None
Extracted molecule total RNA
Extraction protocol RNA extraction and preparation of cDNA library for sequencing: Embryonic tissues (endoderm and ectoderm, as indicated) were dissected from embryos at the respective stage and frozen at -80°C. One tissue from one embryo was processed individually. RNA extractions were performed using Qiagen RNeasy Mini kit (Qiagen, 74106) according to the manufacturer's protocol including the DNase step. RNA was eluted in 40ul of DEPC H2O and 500 ng RNA was used to generate a cDNA sequencing library with Illumina TruSeq kit (RS-122-2001), according to the manufacturer's protocol.
Library construction: Illumina TruSeq RNA sample prep kit for RNA-seq.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Fastq files processed by filtering out low-quality reads (<Q20) and low-quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to X. laevis genome 6.1 using TopHat 2.0.6.
ChIP-seq data have been aligned to X. laevis genome 6.1 using BWA 0.6.2 with default options. Duplicate reads were then removed.
Peaks were called using MACS2 2.0.9 with --broad options and q-value<0.01.
Differential analysis was conducted using EdgeR package.
The 553,960 assembled transcripts were provided by the International Xenopus Genome Project (http://www.marcottelab.org/index.php/Xenopus_Genome_Project) in October 2012. This assembly was augmented with Xenopus laevis sequences from the NCBI RefSeq database downloaded in February 2012 (30,611 sequences). The combined transcript sequences were filtered with cd-hit-est 4.5.7 (Li and Godzik, 2006) with a similarity score of 95% to remove redundant sequences. This resulted in a final set of 39,384 transcripts. To provide gene names, orthologs were found against the M. musculus proteome (downloaded in January 2013 - NCBI RefSeq) using Inparanoid 4 (Alexeyenko et al. 2006) on predicted ORFs from the Trinity Suite (Grabherr et al. 2011). The sequences were further annotated using InterProScan 4.8 (Zdobnov and Apweiler, 2001) to provide both InterPro Domains (Release 35) and Panther 7.2 ontology terms (Thomas et al. 2003). Xenopus laevis NCBI Descriptions were provided for transcripts that originated at the NCBI. The gtf file containing this information is reported as supplementary material of the previous study: PMID: 27034506, DOI: 10.1101/gr.201541.115.
Genome_build: X. laevis genome 6.1 (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.1/)
Supplementary_files_format_and_content: *.xls: Excel files contain raw counts.
Supplementary_files_format_and_content: *.bed: BED files contain coordinates of broad peaks called with MACS2 (2.0.9).
 
Submission date Dec 13, 2016
Last update date May 15, 2019
Contact name Angela Simeone
E-mail(s) angela.simeone@gmail.com
Organization name University of Cambridge
Department Cancer Research UK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL21046
Series (1)
GSE92366 H3K4 Methylation-Mediated Memory of an Active Transcriptional State Impairs Nuclear Reprogramming
Relations
BioSample SAMN06141041
SRA SRX2422272

Supplementary file Size Download File type/resource
GSM2428226_SLX-9430.C5V29ANXX.s_2.r_1.Index2.QCed.bamcountTabPipe.xls.gz 279.9 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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