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Sample GSM1576857 Query DataSets for GSM1576857
Status Public on Oct 01, 2015
Title MEFs
Sample type SRA
Source name embryonic fibroblasts
Organism Mus musculus
Characteristics strain: C57BL/6 x 129
cell type: embryonic fibroblasts
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 Dec 27, 2021
Contact name Yossi buganim
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
Reanalyzed by GSE192652
BioSample SAMN03275642
SRA SRX836155

Supplementary file Size Download File type/resource
GSM1576857_S10_MEFs.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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