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Sample GSM1598294 Query DataSets for GSM1598294
Status Public on Nov 30, 2015
Title S13
Sample type SRA
 
Source name Human zygote (2PN)
Organism Homo sapiens
Characteristics tissue type: embryo
developmental stage: 2PN zygote
predicted viability: bad
Treatment protocol micropipette aspiration to measure mechanical parameters
Extracted molecule total RNA
Extraction protocol SMARTer® Ultra™ Low RNA kit (Clontech)
NEBNext® DNA Sample Prep Master Mix Set (New England Biolabs)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Adapter clipping and trimming using fastq_quality_trimmer and fastx_clipper
Align reads to hg18 using STAR aligner
Convert files from sam to bam format and sort reads by name
Output read counts using HTSeq-count
Obtain adjusted expression values using edgeR and ComBat packages in R
Genome_build: hg18
Supplementary_files_format_and_content: Processed files contain read counts for each gene ([sample name]_paired_count.txt). There is also a file adjusted_expression_data.txt which contains all the data values used to generate figures along with adjusted_expression_qvals.txt which contains the q-values for all genes.
 
Submission date Jan 30, 2015
Last update date May 15, 2019
Contact name Livia Zarnescu Yanez
E-mail(s) livia.z.yanez@gmail.com
Organization name Stanford University
Department Bioengineering
Lab Camarillo Lab
Street address 443 Via Ortega
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platform ID GPL11154
Series (1)
GSE65481 Human Embryo Single Cell Transcriptome Analysis
Relations
BioSample SAMN03322776
SRA SRX861650

Supplementary file Size Download File type/resource
GSM1598294_S13_paired_count.txt.gz 91.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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