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Sample GSM6597872 Query DataSets for GSM6597872
Status Public on Sep 13, 2023
Title 3-150-2_Prog_N1: progenitors, wildtype core // progenitors, rep 1
Sample type SRA
 
Source name Isolated from wildtype Achilles tendon
Organism Mus musculus
Characteristics tissue: Isolated from wildtype Achilles tendon
cell type: Tendon progenitors (mixed)
genotype: B6.129S2-Il6tm1Kopf/J Il-6+/+
treatment: in a hydrogel surrounding a wildtyp core explant
Treatment protocol Treatment consisted of co-culture with different extrinsic cell populations and integration of core explants unable to express interleukin-6 (IL-6)
Growth protocol Hybrid explant // hydrogel constructs were clamped and maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), antibiotics, and L-ascorbic acid (200 μM) in humidified atmosphere with 5% CO2 at 37C for 7 days
Extracted molecule total RNA
Extraction protocol The samples were snap-frozen in liquid nitrogen, pulverized by cryogenic grinding (FreezerMill 6870, SPEXTMSamplePrep), and further processed with the RNeasy micro kit (Qiagen)
The RNA libraries were prepared using Illumina's Stranded Total RNA Prep with Ribo-Zero Plus.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Illumina Truseq Total RNA (ribosomal depletion)
Data processing The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) or reads shorter than 30nt using Fastp (v0.20).
Pseudoalignment and calculation of transcript abundance based on the high quality reads was performed with Kallisto (v0.46.1) using the GENCODE annotation of release M26 for the mouse genome GRCm39.
Differential expression analysis was performed with DESeq2 (R4.1.2, v1.34).
All previous steps were performed using the SUSHI framework at the Functional Genomics Center Zurich.
Assembly: GRCm39
Supplementary files format and content: .txt : text file containing trancript identifiers (ENSEMBL ID) and the match counts based on Kallisto
Supplementary files format and content: .xlsx : Microsoft Excel Worksheet containing the DEG data based on DESeq2 (i.e. gene_id, gene_name, GO, gnc_symbol, entrez_id, log2 ratio, pValue, fdr)
 
Submission date Sep 23, 2022
Last update date Sep 13, 2023
Contact name Tino Stauber
E-mail(s) staubert42@gmail.com
Organization name ETH Zurich
Street address Lengghalde 5
City Zurich
ZIP/Postal code 8008
Country Switzerland
 
Platform ID GPL24247
Series (1)
GSE214015 Il-6 signaling exacerbates hallmarks of tendon lesions by stimulating progenitor proliferation & migration to damage.
Relations
BioSample SAMN30983651
SRA SRX17681523

Supplementary file Size Download File type/resource
GSM6597872_3-150-2_Prog_N1.txt.gz 126.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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