|
Status |
Public on Dec 16, 2022 |
Title |
K27me3 Epigenomic MERFISH Rep2 |
Sample type |
SRA |
|
|
Source name |
hTERT immortalized RPE1 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: RPE1 histone mark: K27me3
|
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
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|
|
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 |
SAMN30351283 |
SRA |
SRX17106368 |