|
| Status |
Public on Apr 08, 2024 |
| Title |
116_mRNA_gDNA-seq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
molecule: mRNA gDNA
treatment: untreatment
|
| Extracted molecule |
other |
| Extraction protocol |
Nucleic acid was extracted by SDS
gDNA library, mRNA library and mRNA&gDNA library were constructed by extracting whole nucleic acid from cells. RNase A enzyme is used to remove RNA from gDNA library. Genome DNA was removed by digested with DNase I in mRNA library while retained in mRNA&gDNA library as internal reference. mRNA was reverse-transcribed with oligo(dT) as the primer to synthesis the first strand of the complementary DNA (cDNA). To reduce bias and simplify our pipeline, fragmented cDNA without second strand synthesis and gDNA were denatured by heat following library preparation using a high-efficient ssDNA ligation technique, Adaptase from Accel-NGS 1S Plus DNA Library Kit (Swift Accel-NGS).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads are mapped to h38 using HISTAT2(version 2.2.1) with default parameters
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
BigWig files were generated by using deepTools (version 3.5.1)
Assembly: GRCh38
|
| |
|
| Submission date |
Jan 18, 2023 |
| Last update date |
Apr 08, 2024 |
| Contact name |
Zhenzhen Wang |
| E-mail(s) |
wzz02182020@gmail.com
|
| Phone |
+8618790570387
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
97 Buxin Road
|
| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE223145 |
siqRNA-seq is a spike-in-independent technique for quantitative mapping of mRNA landscape |
|
| Relations |
| BioSample |
SAMN32781773 |
| SRA |
SRX19061137 |
