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GSE143437

GSE GEO
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Single-cell transcriptomic atlas of the mouse regenerating muscle tissue

Organism: Mus musculus
Platform: GPL19057
Samples: 10
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jan 10 2020
Last Updated: Jan 30 2025
Status: Public on Jan 11 2020
Contact: Andrea,J,De Micheli (Cornell University)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA600499 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP241205

Summary

We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology.

Overall Design

The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.

Analysis (7 steps)

View Data Processing
Processing steps for GSE143437
  1. Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
  2. Sequences were aligned to mm10 using Cell Ranger v2 pipeline (10X Genomics)
  3. Gene expression data was processed with Seurat v2.3.4 (Satija lab) using R v3.6.2 (2019-12-12)
  4. Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 200)
  5. Filtering by percent mitochondiral genes in included cells (maximum 0.2), number of UMIs in included cells (minimum 1000, maximum 60000), and number of mapped genes in included cells (maximum 8000)
  6. Log-normalization of expression data
  7. Cell annotations in metadata derived from unsupervised clustering in CCA space (CCA coefficients obtained by MultiCCA from Seurat (Satija Lab).

Supplementary Files (3)

GSE143437_DeMicheli_MuSCatlas_metadata.txt.gz Download
GSE143437_DeMicheli_MuSCatlas_normalizeddata.txt.gz Download
GSE143437_DeMicheli_MuSCatlas_rawdata.txt.gz Download
GEO Samples (10)
GSM4259473 GSM4259474 GSM4259475 GSM4259476 GSM4259477 GSM4259478 GSM4259479 GSM4259480 GSM4259481 GSM4259482

Dataset Citations (5)

PubMed citation (PMID 32160558)
PubMed citation (PMID 32624006)
PubMed citation (PMID 35789856)
PubMed citation (PMID 37292698)
PubMed citation (PMID 39578558)

SRA Experiments (10) and Runs (10)

Total: 131096 MB
SRX7540275 SRP241205 RNA-Seq PAIRED
GSM4259473: D0_A; Mus musculus; RNA-Seq
Sample: SRS5978850
BioProject: PRJNA600499
BioSample: SAMN13824791
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 7 months
Sex: female
injury: No injury (Day 0)
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870296 228700456 21040441952 12657.31 Sample_77904_HCNLTBGX7_D0_A_I1.fastq.gz, Sample_77904_HCNLTBGX7_D0_A_… SRA
SRX7540276 SRP241205 RNA-Seq PAIRED
GSM4259474: D0_B; Mus musculus; RNA-Seq
Sample: SRS5978851
BioProject: PRJNA600499
BioSample: SAMN13824790
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 7 months
Sex: female
injury: No injury (Day 0)
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870297 256778531 23623624852 14068.9 Sample_77905_HCNLTBGX7_D0_B_I1.fastq.gz, Sample_77905_HCNLTBGX7_D0_B_… SRA
SRX7540277 SRP241205 RNA-Seq PAIRED
GSM4259475: D0_Cv3; Mus musculus; RNA-Seq
Sample: SRS5978852
BioProject: PRJNA600499
BioSample: SAMN13824789
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 5 months
Sex: female
injury: No injury (Day 0)
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870298 237783790 21638324890 12178.17 Sample_87381_HH3Y5BGX9_D0_Cv3_I1.fastq.gz, Sample_87381_HH3Y5BGX9_D0_… SRA
SRX7540278 SRP241205 RNA-Seq PAIRED
GSM4259476: D2_C; Mus musculus; RNA-Seq
Sample: SRS5978853
BioProject: PRJNA600499
BioSample: SAMN13824798
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: female
injury: Notexin, day 2 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870299 143080183 13163376836 8188.74 Sample_79500_HGLYTBGX7_D2_C_I1.fastq.gz, Sample_79500_HGLYTBGX7_D2_C_… SRA
SRX7540279 SRP241205 RNA-Seq PAIRED
GSM4259477: D2_D; Mus musculus; RNA-Seq
Sample: SRS5978854
BioProject: PRJNA600499
BioSample: SAMN13824797
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: female
injury: Notexin, day 2 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870300 243114255 22366511460 13294.19 Sample_84097_HMYLYBGX7_D2_D_I1.fastq.gz, Sample_84097_HMYLYBGX7_D2_D_… SRA
SRX7540280 SRP241205 RNA-Seq PAIRED
GSM4259478: D5_A; Mus musculus; RNA-Seq
Sample: SRS5978855
BioProject: PRJNA600499
BioSample: SAMN13824796
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: male
injury: Notexin, day 5 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870301 360147131 33133536052 20546.9 Sample_79493_HV5VGBGX7_D5_A_I1.fastq.gz, Sample_79493_HV5VGBGX7_D5_A_… SRA
SRX7540281 SRP241205 RNA-Seq PAIRED
GSM4259479: D5_B; Mus musculus; RNA-Seq
Sample: SRS5978856
BioProject: PRJNA600499
BioSample: SAMN13824795
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: female
injury: Notexin, day 5 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870302 219020687 20149903204 12576.6 Sample_79499_HGLYTBGX7_D5_B_I1.fastq.gz, Sample_79499_HGLYTBGX7_D5_B_… SRA
SRX7540282 SRP241205 RNA-Seq PAIRED
GSM4259480: D5_C; Mus musculus; RNA-Seq
Sample: SRS5978857
BioProject: PRJNA600499
BioSample: SAMN13824794
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: male
injury: Notexin, day 5 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870303 214150304 19701827968 12388.28 Sample_79495_HV5G3BGX7_D5_C_I1.fastq.gz, Sample_79495_HV5G3BGX7_D5_C_… SRA
SRX7540283 SRP241205 RNA-Seq PAIRED
GSM4259481: D7_C; Mus musculus; RNA-Seq
Sample: SRS5978858
BioProject: PRJNA600499
BioSample: SAMN13824793
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: female
injury: Notexin, day 7 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870304 199316776 18337143392 11501.83 Sample_79496_HV5G3BGX7_D7_C_I1.fastq.gz, Sample_79496_HV5G3BGX7_D7_C_… SRA
SRX7540284 SRP241205 RNA-Seq PAIRED
GSM4259482: D7_D; Mus musculus; RNA-Seq
Sample: SRS5978859
BioProject: PRJNA600499
BioSample: SAMN13824792
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
genotype: C57Bl/6
age: 4 months
Sex: male
injury: Notexin, day 7 post-injury
Original files (1)
Tibialis anterior muscle
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10870305 250241224 23022192608 13695.52 Sample_84098_HMYLYBGX7_D7_D_I1.fastq.gz, Sample_84098_HMYLYBGX7_D7_D_… SRA

Linked Publications (1)

Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
Proceedings of the National Academy of Sciences of the United States of America · 2024

Data Files (10)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Sample_77904_HCNLTBGX7_D0_A_I1.fastq.gz RNA-Seq 12.4 GB link
— Sample_77905_HCNLTBGX7_D0_B_I1.fastq.gz RNA-Seq 13.7 GB link
— Sample_79493_HV5VGBGX7_D5_A_I1.fastq.gz RNA-Seq 20.1 GB link
— Sample_79495_HV5G3BGX7_D5_C_I1.fastq.gz RNA-Seq 12.1 GB link
— Sample_79496_HV5G3BGX7_D7_C_I1.fastq.gz RNA-Seq 11.2 GB link
— Sample_79499_HGLYTBGX7_D5_B_I1.fastq.gz RNA-Seq 12.3 GB link
— Sample_79500_HGLYTBGX7_D2_C_I1.fastq.gz RNA-Seq 8.0 GB link
— Sample_84097_HMYLYBGX7_D2_D_I1.fastq.gz RNA-Seq 13.0 GB link
— Sample_84098_HMYLYBGX7_D7_D_I1.fastq.gz RNA-Seq 13.4 GB link
— Sample_87381_HH3Y5BGX9_D0_Cv3_I1.fastq.gz RNA-Seq 11.9 GB link