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Sample GSM1598303 Query DataSets for GSM1598303
Status Public on Nov 30, 2015
Title S22
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
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
BioSample SAMN03322773
SRA SRX861659

Supplementary file Size Download File type/resource
GSM1598303_S22_paired_count.txt.gz 92.8 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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