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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 18, 2023 |
| Title |
Camellia-seq-lineage_LL731-P2-TC |
| Sample type |
SRA |
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| Source name |
BoneMarrow-HSC
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| Organism |
Mus musculus |
| Characteristics |
cell type: BoneMarrow-HSC
carlin protocol: Camellia-seq_CARLIN_RNA
carlin locus: TC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each sample has its corresponding CARLIN protocol as shown above. The CARLIN DNA or RNA materials are extracted from either 1) bulk cell populations sorted with FACS or 2) single-cell samples prepared with 10X encapsulation or individually sorted single cells from Camellia-seq
We used bulk RNA or DNA as starting material. RNA were converted to DNA with SuperScrit III. Then we used a nested PCR approach with locus specific primers to perform targeted amplification with Q5 High-Fidelity DNA Polymerase (New England Biosciences, M0491L). We used 1.5X Ampure XP beads (Beckman Coulter, A63881) to purify the PCR product from each step once except the final indexing PCR product (0.8X, twice purification). The final indexing libraries were pooled and quantified (Kappa Biosystems, KK4835) and sequenced on Illumina MiSeq using paired-end 500 cycles v2 kits (Illumina, MS-102-2003) with 5% PhiX sequencing control v3 (Illumina, FC-110-3001).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
DATA are processed with CARLIN pipeline, except CARLIN libraries from Camellia-seq, which were analyzied with a customized script.
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| Submission date |
Jan 09, 2023 |
| Last update date |
Oct 18, 2023 |
| Contact name |
SHOU-WEN WANG |
| E-mail(s) |
wangshouwen@westlake.edu.cn
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| Organization name |
Westlake University
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| Street address |
Shilongshan ST #18, Xihu District
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| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310024 |
| Country |
China |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE222479 |
A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells |
| GSE222486 |
A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells |
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| Relations |
| BioSample |
SAMN32644463 |
| SRA |
SRX18983061 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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