 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 03, 2019 |
| Title |
hKRT_Mi2KD_Exp2_RNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
neonatal foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
cell types: keratinocytes
genotype: Mi2KD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary human epidermal keratinocytes were incubated for 6 hours with the infection medium containing lentiviral particles derived from shRNA lentiviral constructs for Mi-2β and/or cJUN or control, and then selected for 3-5 days in puromycin.
Trueseq stranded mRNA sample prep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) or hg19 (human genome) assembly using the genome mappers Bowtie2 for ATACseq and STAR for RNAseq and ChIPseq.
For RNA-seq, read normalization, RPKM and differential gene expression, were performed using the HOMER scripts analyzeRepeats.pl and getDiffExpression.pl with implementation of DESeq2 through R.
Peak calling for ATAC-seq was perfomed using MACS2 call peaks with --keep-dup all --nomodel --shift 37 --extsize 73.
Peak calling for ChIP-seq was performed using the Homer findPeaks algorithm.
Genome_build: mm10, hg19
|
| |
|
| Submission date |
Oct 31, 2019 |
| Last update date |
Dec 03, 2019 |
| Contact name |
Katia Georgopoulos |
| E-mail(s) |
[email protected]
|
| Phone |
617-7264445
|
| Organization name |
Harvard Medical School
|
| Department |
CBRC
|
| Lab |
Georgopoulos
|
| Street address |
1st and 13th St
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE139685 |
Functional interactions between Mi-2β and AP1 complexes control response and recovery from barrier disruption |
|
| Relations |
| BioSample |
SAMN13173362 |
| SRA |
SRX7082291 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
