|
| Status |
Public on Apr 25, 2024 |
| Title |
CON_2_IP |
| Sample type |
SRA |
| |
|
| Source name |
Skin or mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adjcent mucocal tissues
rip antibody: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)
|
| 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 NovaSeq 6000 |
| |
|
| 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
ABLIRC strategy was used to identify the binding regions of RBP on genome (Xia et al., 2017a). Reads with at least 1 bp overlap were clustered as peaks. For each gene, computational simulation was used to randomly generated reads with the same number and lengths as reads in peaks. The outputting reads were further mapped to the same genes to generate random max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p-value < 0.05) were selected. The IP and input samples were analyzed by the simulation independently, and the IP peaks that have overlap with Input peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak data
|
| |
|
| 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 |
GPL24676 |
| Series (2) |
| GSE172139 |
Expression profile analysis of long non-coding RNAs in condyloma acuminatum in a Chinese female population by RNA-sequencing and bioinformatics [clip-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 |
SAMN18747399 |
| SRA |
SRX10606433 |
