|
| Status |
Public on May 09, 2024 |
| Title |
H3K36ME3 Cut&Tag of LCLs, NA18504 |
| Sample type |
SRA |
| |
|
| Source name |
NA18504
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NA18504
cell type: Lymphoblastoid cell lines (LCLs)
antibody: H3K36ME3
|
| Biomaterial provider |
Coriell Cell Repositories https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA18504&Product=DNA
|
| Growth protocol |
LCLs were grown in RPMI + glutamine + Penn/Strep + 20% FBS. Cells were grown in 4 batches, with approximately 20-35 cell lines per batch. For Cut&Tag, 100,000 cells were frozen in 10% DMSO.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut&Tag was performed as described in DOI: dx.doi.org/10.17504/protocols.io.z6hf9b6 using polyclonal antibodies.
14 PCR cycles were performed for amplification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Cut&Tag reads were aligned to the genome using HISAT 2.2.1.
H3K36ME3 counts overlapping gene bodies were obtained using bedtools multicov.
Counts were transformed first into counts per million (CPM) across each sample. log2 CPM counts were then normalized with standard normalization for each gene. Finally, we used rank normalization acros each sample to enforce normality to the distribution.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for Cut&Tag data
Supplementary files format and content: tab-delimited text file includes normalized counts for Cut&Tag data
Library strategy: Cut&Tag
|
| |
|
| Submission date |
Dec 26, 2023 |
| Last update date |
May 09, 2024 |
| Contact name |
Carlos F Buen Abad Najar |
| E-mail(s) |
cnajar@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Medicine
|
| Lab |
The Li lab
|
| Street address |
920 E 58th St
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE252003 |
Cryptic splicing mediates genetic and therapeutic perturbation of human gene expression levels [Cut&Tag] |
| GSE252006 |
Global impact of unproductive splicing on human gene expression. |
|
| Relations |
| BioSample |
SAMN37560896 |
| SRA |
SRX21903196 |
