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| Status |
Public on Jun 06, 2021 |
| Title |
ESC_2i_PacBio_subreads |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
cell culture: 2i grown
treatment: untreated
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| Treatment protocol |
no treatment
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| Growth protocol |
mouse Embryonic stem cells were cultured on gelatin in 2i conditions
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
polyA+ extracted RNA
mRNAs were amplified using the Clontech SMARTer PCR cDNA Synthesis Kit with 9 cycles and used in the SMRTbell library prep.
Pacbio library sequenced on the SMRTseq 2000 platform
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Sequel |
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| Data processing |
Library strategy: Iso-Seq
PacBio reads were processed using the SMRTLINK v8.0.0 IsoSeq3 pipeline.
Circular consensus sequences (CCS) were generated using default parameters (--minPasses = 1, --min-rq = 0.8, CCS Polish = No). ).
FLNC were determined through further refining using lima (removal of adapters and correct orientation of sequences), poly-A trimming and concatemer removal
FLNC reads were then aligned to the mm10 genome using Minimap2 with the following parameters (-ax splice, -uf, -k14).
Results were visualized in Integrated Genome Viewer (v2.4.19).
Genome_build: mm10
Supplementary_files_format_and_content: Isoseq_flnc-vs-genome.sort.bam file contains the processed flnc reads representing the Pacbio isoforms after processing through Isoseq3 pipeline
Isoseq_flnc-vs-genome.sort.bam.bai is the index for the above file, for visualisation in a genome browser
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| Submission date |
Oct 29, 2020 |
| Last update date |
Jun 06, 2021 |
| Contact name |
Suzana Hadjur |
| E-mail(s) |
s.hadjur@ucl.ac.uk
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| Phone |
+44 7798957199
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| Organization name |
Ucl
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| Department |
Cancer biology
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| Lab |
Genome organization
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| Street address |
72 Huntley street
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| City |
London |
| ZIP/Postal code |
Wc1e6bt |
| Country |
United Kingdom |
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| Platform ID |
GPL24198 |
| Series (2) |
| GSE160387 |
STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq] |
| GSE160390 |
PEZIC_STAG1_Pluripotency |
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| Relations |
| BioSample |
SAMN16591564 |
| SRA |
SRX9397318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4872530_Isoseq_flnc-vs-genome.sort.bam |
133.7 Mb |
(ftp)(http) |
BAM |
| GSM4872530_Isoseq_flnc-vs-genome.sort.bam.bai.gz |
128.6 Kb |
(ftp)(http) |
BAI |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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