|
| Status |
Public on Dec 16, 2022 |
| Title |
K27ac Epigenomic MERFISH Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hTERT immortalized RPE1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RPE1
histone mark: K27ac
|
| Treatment protocol |
No treatment was done on the RPE1 cells. The cells were plated at a density of 1 million on silanized coverslip.
|
| Growth protocol |
RPE1 cells were DMEM-F12 media with 10% FBS and 1%PenStrep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted using Zymo RNA kit
Reverse transcription was performed on the RNA using Maxima RT kit. The cDNA was amplified adding in the illumina adapters.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CUT&Tag reaction (ChIP-seq) with a T7 sequence added to transposed adapter to amplify the tagged region (with the histone marks). The resulting RNA is subjected to reverse transcription and followed by PCR for RNA-sequencing. Detailed protocol from the paper attached as a supplementary PDF file.
|
| Data processing |
Sequencing reads were mapped using Bowtie 2.1.041 with an additional -5 10 parameter to remove the low-quality bases and the following additional option (--very-sensitive)
Mitochondrial reads were then removed (awk '\$3!="chrM"'). Reads were subsequently deduplicated using the rmdup option in samtools
Peak calling was performed using MACS 2.1.142 using the default options outlined in the vignette with the significant value cut-off at q<0.1
Assembly: hg19
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Aug 16, 2022 |
| Last update date |
Dec 16, 2022 |
| Contact name |
Cheen Euong Ang |
| E-mail(s) |
cang@fas.harvard.edu
|
| Organization name |
Stanford University
|
| Street address |
265 Campus Drive, G3145
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE191069 |
Spatially resolved epigenomic profiling of single cells in complex tissues |
|
| Relations |
| BioSample |
SAMN30351286 |
| SRA |
SRX17106365 |
