|
| Status |
Public on Sep 01, 2021 |
| Title |
fndc-1 KO rep5 |
| Sample type |
SRA |
| |
|
| Source name |
worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/background: N2
genotype: fndc-1(rny14)
age: 1 day adult
tissue: whole worm
|
| Growth protocol |
Non-stress standard conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
OP50 were removed, using liquid nitrogen to flash freeze samples, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
F5
Raw_gene_counts_matrix.txt
|
| Data processing |
Data Formatting: bcltofastq-2.19.0
Data Cleaning: Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment: STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1: subread-1.6.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification2: subread-1.6.1, featurecounts, -M -s 2 -t exon -g gene_name
Genome_build: WBcel235
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Sep 27, 2020 |
| Last update date |
Sep 01, 2021 |
| Contact name |
keith nehrke |
| E-mail(s) |
[email protected]
|
| Phone |
5852757020
|
| Organization name |
University of Rochester Medical Center
|
| Department |
Medicine
|
| Street address |
1514 Rush Scottsville Rd
|
| City |
Rush |
| State/province |
NY |
| ZIP/Postal code |
14543 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE158628 |
FNDC-1-Mediated Mitophagy and ATFS-1 Coordinate to Protect Against Hypoxia-Reoxygenation |
|
| Relations |
| BioSample |
SAMN16276712 |
| SRA |
SRX9200040 |
