|
| Status |
Public on Mar 30, 2023 |
| Title |
INV_H9_RNA-seq_rep1 [AWIL093] |
| Sample type |
SRA |
| |
|
| Source name |
edited H9 hESC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: edited H9 hESC
genotype: Hemizygous inversion
differentiation day: d0
|
| Treatment protocol |
Gene editing by nucleofection
|
| Growth protocol |
Cultured in Essential 8 media (Gibco, A1517001) on Matrigel substrate (Corning, 354277)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy kit (Qiagen, 217004) with on-column DNAse I treatment (RNase-free DNase Set (Qiagen, 79254) )
Illumina TruSeq stranded RNA-seq library preparation kit (Illumina, RS-122-2101)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
RNA-seq from H9 hESCs with an inversion on Chr7 due to CRISPR/Cas9 editing
|
| Data processing |
STAR (v. 2.7.1a ) example command: STAR --runThreadN 8 --outTmpDir ~/STARtemp --genomeDir $GENOMEDIR --readFilesIn $FASTQDIR/paired_Sample11_S11_R1.fastq.gz $FASTQDI R/paired_Sample11_S11_R2.fastq.gz --outFileNamePrefix $ANALYSISDIR/paired_Sample11_S11 --readFilesCommand zcat --sjdbGTFfile $GTFF ILE --outSAMprimaryFlag OneBestScore --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhang Min 2 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype B AM SortedByCoordinate --outSAMattributes Standard --outWigType bedGraph --outWigStrand Stranded --outWigNorm RPM rm -r ~/STARtemp
featureCounts (subread v. 2.0)
Differential gene expression with DESeq2 (v. 1.26.0)
Correction for surrogate variables with sva (3.34.0)
mm10 or hg19
text files of counts to be used with DESeq2
|
| |
|
| Submission date |
Mar 10, 2022 |
| Last update date |
Mar 30, 2023 |
| Contact name |
Justin Cotney |
| Organization name |
UConn Health
|
| Department |
Genetics and Genome Sciences
|
| Street address |
400 Farmington Avenue
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-6403 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE198297 |
Chromatin state and chromatin architecture in mouse embryonic craniofacial tissue, neural crest cell culture model and human primary craniofacial tissue |
|
| Relations |
| BioSample |
SAMN26559542 |
| SRA |
SRX14427331 |
