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| Status |
Public on Jan 07, 2021 |
| Title |
Cortex P56 CASTxB6 Cell 001 |
| Sample type |
SRA |
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| Source name |
cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: cortex
age: P56
strain: CASTxB6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
[Isolation of cell nuclei] Cell nuclei were isolated based on protocols from (Krishnaswami et al., 2016; Lacar et al., 2016) with minor modifications. In particular, Tris buffer would react with formaldehyde, and was therefore substituted with equal molarity of HEPES buffer. See details below: Cortex and hippocampus were dissected in ice-cold PBS, and placed in 2 mL nuclei isolation medium with Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT, 0.1% Triton X-100) in a 2 mL Dounce homogenizer (Sigma D8938). Note that DTT concentration was not specified in (Krishnaswami et al., 2016); here we used 1 uM from (Lacar et al., 2016). Tissues were homogenized with 5 strokes of the loose (A) pestle, and 15 strokes of the tight (B) pestle. The homogenate was centrifuged for 8 min at 94 g, 4 C, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei isolation medium without Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT). The tube was centrifuged for 8 min at 94 g, 4 C again, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei storage buffer (0.1665 M sucrose, 5 mM MgCl2, 10 mM HEPES pH 8.0), and filtered with 40 um. Note that sucrose concentration was not specified in (Krishnaswami et al., 2016); here we used 0.1665 M from (Lacar et al., 2016). Also note that the recipe in (Lacar et al., 2016) seems to have typos in some ingredient volumes; here we followed the final concentrations. [Fixation of cell nuclei] Nuclei were fixed according to our Dip-C protocol (Tan et al., 2019) with minor modifications. In particular, nuclei were fixed directly in the 1 mL nuclei storage buffer (with HEPES instead of Tris buffer; see above) rather than switching to PBS; and centrifugation was performed at 1,000 g rather than 600 g. See detailed below: Nuclei were directly in the nuclei storage buffer (1 mL) with the addition of 66.7 uL 32% PFA (EMS 15714) to a final concentration of 2%. The tube was rotated for 10 min at room temperature; and 200 uL 1% BSA in PBS was then added. The tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant removed. The pellet was resuspended in 1 mL ice-cold 1% BSA in PBS. Nuclei were counted and aliquoted to up to 0.5 million per tube. Each tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant was removed. The pellet was stored at -80 C. [Diploid chromatin conformation Capture (Dip-C)] A pellet of fixed cell nuclei was thawed on ice. We then proceeded directly to the step where 50 uL 0.5% SDS was added in the Dip-C protocol (Tan et al., 2019) and followed through with no modifications. Cells were sorted on a Beckman Coulter MoFlo Astrios, and amplified with homemade Nextera.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
cortex-p056-cb_001
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| Data processing |
Library strategy: Dip-C
Please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: Please see 00README.md
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| Submission date |
Mar 04, 2020 |
| Last update date |
Jan 07, 2021 |
| Contact name |
Longzhi Tan |
| E-mail(s) |
tanlongzhi@gmail.com
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| Organization name |
Harvard University
|
| Department |
Chemistry and Chemical Biology
|
| Lab |
Xiaoliang Sunney Xie
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| Street address |
12 Oxford St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE146397 |
Diploid chromatin conformation capture (Dip-C) of single cells from the developing mouse cortex and hippocampus |
| GSE162511 |
Single-cell transcriptome and 3D genome atlas of the developing mouse brain |
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| Relations |
| BioSample |
SAMN14129476 |
| SRA |
SRX7743824 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4382869_cortex-p056-cb_001.20k.1.3dg.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.1.clean.3dg.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.2.3dg.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.2.clean.3dg.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.3.3dg.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.3.clean.3dg.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.4.3dg.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.4.clean.3dg.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.5.3dg.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.20k.5.clean.3dg.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.contacts.hic |
10.4 Mb |
(ftp)(http) |
HIC |
| GSM4382869_cortex-p056-cb_001.contacts.pairs.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.contacts.seg.txt.gz |
12.4 Mb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.cpg_b100k.color2.txt.gz |
172.7 Kb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.cpg_b1m.color2.txt.gz |
26.4 Kb |
(ftp)(http) |
TXT |
| GSM4382869_cortex-p056-cb_001.impute.pairs.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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