NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5291265 Query DataSets for GSM5291265
Status Public on May 11, 2024
Title Day_12_FSHD2_4_R1
Sample type SRA
 
Source name Primary myoblasts from quadricep biopsy
Organism Homo sapiens
Characteristics cell line: FSHD2-4
day of differentiation: Day 12
fshd status: FSHD2
muscle source: quadricep
library prep kit: Nextera DNA Flex Library Prep Kit (20018704, Illumina)
Extracted molecule polyA RNA
Extraction protocol Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).
RNA was converted to cDNA using the Smart-Seq 2 protocol (Picelli, et al., Nat. Protoc., 2014). Libraries were constructed with the Nextera DNA Library Prep Kit (Illumina) for days 0 to 5 for FSHD2-3. The Nextera DNA Flex Library Prep Kit (Illumina) was used for all other RNA-seq samples. Libraries were sequenced on the Illumina NextSeq500 with paired-end 43 bp reads to a depth of 5 to 40 million reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) with defaults with gene annotations for protein coding genes and lncRNAs from GENCODE v28. Results were output as counts, and effective gene length was used after normalization to compute transcripts per million (TPM).
Counts were batch corrected for the two different library prep methods using ComBat-seq from sva (version 3.36.0).
Genes were filtered for 10 counts in all samples of at least one condition (same FSHD status, muscle group and differentiation day) using filterByExpr from edgeR (version 3.30.3).
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM.
 
Submission date May 12, 2021
Last update date May 11, 2024
Contact name Ali Mortazavi
E-mail(s) ali.mortazavi@uci.edu
Organization name UC Irvine
Street address 2300E Biological Sciences 3
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL18573
Series (2)
GSE174301 Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD [expression]
GSE174370 Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD
Relations
BioSample SAMN19114904
SRA SRX10853041

Supplementary file Size Download File type/resource
GSM5291265_Day_12_FSHD2_4_R1_rsem.genes.results.gz 848.5 Kb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap