|
| Status |
Public on Sep 07, 2024 |
| Title |
RSeT H9, rep3 Nucleolar DNA |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: Human embryonic stem cells
cell state: Naïve
fraction: nucleolar DNA
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Naïve and primed H9 hES cells maintained in RSeT and mTeSR, respectively, following manual instruction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were extracted with the TakaRa NucleoBond AGX-20 columns (TakaRa # 740544) and corresponding NucleoBond® Buffer Set III (TakaRa # 740603), following the manual instructions.
Libraries were constructed using Illumina`s TruSeq DNA PCR-free Library Preparation kit (Illumina # 20015962), and 350 bp fragments were sonicated and size-selected by sample-purifying beads following manual instruction.
DNA PCR-free Library
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
final_naive_NAD.bed
|
| Data processing |
the raw sequencing datas were processed using bwa, then filtered using samtools 1.10 (by “samtools view -b -F 4 -q 10”) to generate bam files.
The bam files were processed with Epic2 to call the NADs with parameters bin_size=10000, gap=5.
The final_NADs files were called if two of three applicated samples were called in the NADs.
Assembly: hg38
Supplementary files format and content: bed
Library strategy: NAD-seq
|
| |
|
| Submission date |
Jun 30, 2023 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Juan Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
LTRI
|
| Street address |
25 Orde Street, Room 6-1001 MRS
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3H7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE232939 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs |
| GSE236234 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [NAD-seq] |
|
| Relations |
| BioSample |
SAMN36150546 |
| SRA |
SRX20837440 |
