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Sample GSM1576855 Query DataSets for GSM1576855
Status Public on Oct 01, 2015
Title TSCendo-B6#1
Sample type SRA
 
Source name endogenous trophoblast stem cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: endogenous trophoblast stem cells
Growth protocol TSCs and iTSCs were cultured under TX medium condition as decribed in PMID:24527396. mESCs were cultured in 2i medium and MEFs with DMEM supplemenated with 10% FBS medium
Extracted molecule total RNA
Extraction protocol Cells were homogenized and RNA was harvested using the RNeasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina bcl2fastq, v2.15.0.4, was used for transforming basecalls to fastq files.
Sequenced reads were quality trimmed at both ends with PHRED score threshold of 32, trimmed for adaptor sequence with Trim Galore, v0.3.7, and filtered for low-quality reads with the FASTX package, v0.0.13. Reads were then mapped to GRCm38 (mouse) using TopHat v2.0.11 with parameters -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 18 --read-realign-edit-dist 5 --b2-i S,1,0.75 --b2-mp 3,1 --b2-score-min L,-0.5,-0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Cufflinks package v2.2.1 with the programs cuffquant and cuffnorm, using parameters -b, -u and a masking file with all IG, TR, rRNA, tRNA, miRNA, snRNA, snoRNA and pseudo entries of the mouse GTF file.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts and FPKM values at gene level for each sample. Fields are Ensembl_Gene_ID, Ensembl_Transcript_ID, Gene_Full_Name, Gene_Symbol, Gene_Biotype, EntrezGene_ID, RefSeq_mRNA, UCSC_ID, First_replicate_count, Second_replicate_count, First_replicate_fpkm, Second_replicate_fpkm. Multiple data is separated by semicolon. Missing data is represented by a question mark.
 
Submission date Jan 05, 2015
Last update date May 15, 2019
Contact name Yossi buganim
E-mail(s) yossibug@ekmd.huji.ac.il
Organization name The Hebrew University of Jerusalem
Department Developmental Biology and Cancer Research
Lab Buganim
Street address Ein Karem 91120
City Jerusalem
ZIP/Postal code 91120
Country Israel
 
Platform ID GPL19057
Series (1)
GSE64684 Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells
Relations
Reanalyzed by GSM2587551
BioSample SAMN03275641
SRA SRX836153

Supplementary file Size Download File type/resource
GSM1576855_S8_TSCendo-B6_1.tsv.gz 1.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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