|
| Status |
Public on Nov 10, 2022 |
| Title |
ARID1A knockdown, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293FRT cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: ARID1A_KD
|
| Treatment protocol |
siRNA transfection for 72 hours
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNA extraction Kit, followed manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
arid1a_kd_1
|
| Data processing |
Paired end reads of 76 bases were sequenced on a NextSeq 500 in mid-output mode. Data was demultiplexed with bcl2fastq2 v2.20.
Data was aligned to the hg38 genome from UCSC using STAR 2.7.3a with annotations from Ensembl 102, with the following parameters (including end to end alignments): --outSAMprimaryFlag OneBestScore --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.1 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --readFilesCommand zcat --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --alignEndsType EndToEnd
Downstream analysis was done in R 4.0.0 with edger 3.30.3
Assembly: hg38
Supplementary files format and content: raw gene counts generated by STAR for each sample
|
| |
|
| Submission date |
Mar 28, 2022 |
| Last update date |
Nov 10, 2022 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE199631 |
The nuclear granule Paraspeckles interacts with the chromatin remodeling SWI/SNF complex to regulate alternative splicing |
|
| Relations |
| BioSample |
SAMN27025169 |
| SRA |
SRX14639558 |
