|
| Status |
Public on Sep 24, 2019 |
| Title |
m1A-IP-seq, "+AlkB", replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK-293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-293T cells
passages: p15
experimental: m1A-IP-seq, "+AlkB"
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were extracted from HEK-293T cells using the TRIzol reagent and standard protocol; mRNA were enriched by the Dyna-Oligo(dT)25 beads and m1A IP was performed with the m1A antibody.
Libraries were constructed using ligation-based library construction approach incoporating the newly developed RT in the current work.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HZ75
|
| Data processing |
PCR dupilcates were removed by the Raw data (R2 reads of the pair-end data) were first processed with the “clumpify.sh” program in the BBMap package (BBMap-Bushnell B.-sourceforge.net/projects/bbmap/) with the option “dedupe subs=0” to remove PCR duplicates.
Adaptors were trimmed by the “cutadapt” program while reads were filtered by quality and length with options “-a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 20 -m 30”
Reads were aligned to the hg19 genome file downloaded from the UCSC database as well as the known splicing sites via the hisat2 aligner with the option “--trim5 11 ” removing the unique molecular identifier (UMI) sequence and not performing the soft-clipping at the end of reads, with the script “run_cut_alignment_R2_hg19.sh”.
Single base reads counting were performed with bam-readcount.
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing mutation counts at base resolution
|
| |
|
| Submission date |
Jun 18, 2019 |
| Last update date |
Sep 24, 2019 |
| Contact name |
Huiqing Zhou |
| E-mail(s) |
zhouhq@uchicago.edu
|
| Phone |
7343899318
|
| Organization name |
University of chicago
|
| Street address |
LOADING DOCK BEHIND 5741 S DREXEL AVE 929 E 57TH ST
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE123365 |
Evolution of a Reverse Transcriptase to Map N1-Methyladenosine in Human mRNA |
|
| Relations |
| BioSample |
SAMN12086052 |
| SRA |
SRX6087546 |
