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| Status |
Public on Sep 06, 2023 |
| Title |
denervation gastrocnemius snATAC-seq 3 |
| Sample type |
SRA |
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| Source name |
Gastrocnemius muscle
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| Organism |
Mus musculus |
| Characteristics |
tissue: Gastrocnemius muscle
Sex: male
age: 12-week-old
strain: C57BL/6J
treatment: sciatic denervation
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| Treatment protocol |
Mice were anesthetized and the left sciatic nerve was removed for a 2-mm piece. Gastrocnemius (Gas) muscles were harvested 2 weeks after denervation. Gas muscles from left hind limb of normal mice served as controls.
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| Growth protocol |
Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We first prepared nuclei isolation media1 (NIM1: 320 mM sucrose, 25mM KCl, 5 mM MgCl2, and 10 mM Tris buffer, pH=8.0) and homogenization buffer [NIM1 buffer containing 1 µM DTT, 0.4 U/μL RNase Inhibitor (NEB Inc, Ipswich, MA), 0.20U/μL SUPERase-In RNase Inhibitor (Thermo Fisher scientific Inc, Waltham, MA), and 0.1% Triton X-100]. Then, Gas muscles (100~150mg) were minced on ice with a razor blade. Muscles were resuspended in 5 mL ice-cold homogenization buffer and homogenized with a dounce grinder for 12 strokes gently on ice. The homogenate was sequentially filtered through 70 mm and 40 mm cell strainers (pluriSelect, El Cajon,CA) and centrifuged (x1000g) for 5 minutes at 4°C to pellet the nuclei. The pellet was resuspended with 1 mL of ice-cold wash buffer (PBS containing 2% bovine serum albumin and 0.2U/μL ribonuclease inhibitor) and then filtered through the 20μm cell strainer before centrifugation (x500g) for 5 minutes at 4°C. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10 × Genomics, Chromium Single-Cell ATAC kit ) according to the manufacturer’s protocol.
6 snATAC-seq libraries were created with 10X Genomics Chromium Single Cell ATAC v1 chemistry following nuclear dissociation according to the manufacturer's protocol
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10x Genomics
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| Data processing |
Raw sequencing data were processed using Cell Ranger Single Cell Software Suite (v3.0.2) (10x Genomics). The Mus musculus genome reference (mm10) was used for reads alignment in accordance with 10x Genomics recommendations and all reads were mapped to the reference genome using STAR (Spliced Transcripts Alignment to a Reference) with default setting. The mapped reads with valid barcodes and unique molecular identifiers (UMIs) were used to generate the peak-barcode matrix.
Assembly: mm10
Supplementary files format and content: Matrix table with raw peak counts for every region and every nucleus
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| Submission date |
Nov 08, 2022 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Zhaoyong Hu |
| E-mail(s) |
[email protected]
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| Organization name |
Baylor college of medicine
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| Department |
Nephrology
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| Street address |
One Baylor Plaza
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE217575 |
Reprogramming of Cis-regulatory networks during skeletal muscle atrophy [snATAC-seq] |
| GSE217577 |
Reprogramming of Cis-regulatory networks during skeletal muscle atrophy |
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| Relations |
| BioSample |
SAMN31664942 |
| SRA |
SRX18212522 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6721947_6A-SY-N1_barcodes.tsv.gz |
13.2 Kb |
(ftp)(http) |
TSV |
| GSM6721947_6A-SY-N1_matrix.mtx.gz |
83.0 Mb |
(ftp)(http) |
MTX |
| GSM6721947_6A-SY-N1_peaks.bed.gz |
835.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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