|
| Status |
Public on Apr 25, 2024 |
| Title |
CA_5 |
| Sample type |
SRA |
| |
|
| Source name |
Skin or mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: specimen of condyloma acuminatum
|
| Treatment protocol |
CA means specimen of condyloma acuminatum, CON means the adjcent mucocal tissues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue were flash frozen on dry ice, 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 standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2 Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample
|
| |
|
| Submission date |
Apr 15, 2021 |
| Last update date |
Apr 25, 2024 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
|
| Department |
Center for Genome Analysis
|
| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE172137 |
Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics [RNA-seq] |
| GSE172140 |
Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics |
|
| Relations |
| BioSample |
SAMN18747380 |
| SRA |
SRX10606390 |
