|
| Status |
Public on May 11, 2024 |
| Title |
Day_5_FSHD2_3_R2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary myoblasts from quadricep biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: FSHD2-3
day of differentiation: Day 5
fshd status: FSHD2
muscle source: quadricep
library prep kit: Nextera DNA Library Prep Kit (FC-121-1030, 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 |
SAMN19114915 |
| SRA |
SRX10853070 |
