|
| Status |
Public on Jun 06, 2021 |
| Title |
Nanog bait 1_ESC_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
cell culture: 2i-LIF grown
umi-4c bait: Nanog bait 1
|
| Treatment protocol |
untreated
|
| Growth protocol |
Mouse embryonic stem cells (ESC) were cultured in naïve (2i) conditions and neural stem cells were cultured in EGF/FGF media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cell were fixed and extracted nuclei were processed so to capture DNA fragments in close proximity.
Libraries were constructed according to the UMI-4C protocol. Please see methods section of manuscript for further information.
UMI-4C libraries were pooled and sequenced on a HiSeq 2500 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: UMI-4C
UMI-4C raw data were processed using the ‘umi4cPackage’ (v0.0.0.9000) pipeline from the Tanay Lab
To briefly summarize the pipeline
raw reads are parsed through the UMI-4C pipeline, those reads containing the bait and padding sequence are retained and demultiplexed if required
The retained reads are split based on a perfect match to the restriction enzyme sequence to create a segmented fastq file. The first 10 bases of read 2 are extracted and attached to the segments derived from each read pair. Segments are aligned to the mm10 genome using bowtie2.
UMI filtering is used to determine the number of molecules supporting each ligation event, this information is stored in an adj table
The resulting UMI-4C tracks are then imported into R where the molecule counts per ligated fragment can be visualized / interrogated
Genome_build: mm10
Supplementary_files_format_and_content: The final tracks after processing through the umi4cPackage pipeline, converted to a readable text file. Contains the number of molecules supporting each ligation event
|
| |
|
| Submission date |
Oct 25, 2020 |
| Last update date |
Jun 06, 2021 |
| Contact name |
Suzana Hadjur |
| E-mail(s) |
s.hadjur@ucl.ac.uk
|
| Phone |
+44 7798957199
|
| Organization name |
Ucl
|
| Department |
Cancer biology
|
| Lab |
Genome organization
|
| Street address |
72 Huntley street
|
| City |
London |
| ZIP/Postal code |
Wc1e6bt |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE160015 |
STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C] |
| GSE160390 |
PEZIC_STAG1_Pluripotency |
|
| Relations |
| BioSample |
SAMN16539303 |
| SRA |
SRX9353372 |
