|
| Status |
Public on Jan 16, 2023 |
| Title |
embryonic stem cells, ATRA, rep2 [hESC_dTAG-13_ATRA_2] |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: Embryonic Stem Cells
genotype: DNMT3A degradation
treatment: ATRA
time: 12 hours
ir group: hESC_dTAG-13_ATRA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse HSCs and human HSPCs using PicoPure RNA isolation kit (KIT0204). RNA from mESC and hESC was isolated using the Qiagen mini kit
mRNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hESC.txt
Processed tables include the average IR score for each phenotype and group. The intron retention (IR) score was then computed as the ratio of the RPKM-normalized “intronic” read density over the RPKM-normalized “spanning” read density.
|
| Data processing |
Hisat2-aligned reads were filtered for proper-paired reads (-f 2 flag in samtools).
Intron annotations were parsed from RefSeq gene annotation files and were filtered to exclude features that overlap genomic loci on the same strand. Reads mapping to introns were counted using the Python module Pysam (https://github.com/pysam-developers/pysam). For each intron feature, we defined the following two read classes: (1) “intronic” reads mapping at least 6 bases contiguously within the intron and (2) “spanning” reads with ends mapping to the flanking exons. The intron retention (IR) score was then computed as the ratio of the RPKM-normalized “intronic” read density over the RPKM-normalized “spanning” read density. Introns with <10 spanning reads were excluded from all analyses. For analysis of introns with robust changes in expression, a spanning read threshold of 50 was implemented, and only introns with >2-fold changes in the IR score were kept. Statistical analyses were performed using R. Empirical cumulative distributions of IR scores were compared, and p-values estimated using a two-sided Kolmogorov-Smirnov test.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text files include Intron rentention ratios for each Sample
|
| |
|
| Submission date |
Jan 14, 2023 |
| Last update date |
Jan 16, 2023 |
| Contact name |
Margaret Goodell |
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza, N1030
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE222905 |
DNMT3A-coordinated splicing governs the stem state switch toward differentiation in embryonic and hematopoietic stem cells [RNA-seq] |
| GSE222906 |
DNMT3A-coordinated splicing governs the stem state switch toward differentiation in embryonic and hematopoietic stem cells. |
|
| Relations |
| BioSample |
SAMN32739931 |
| SRA |
SRX19035314 |
