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| Status |
Public on Mar 30, 2022 |
| Title |
T200_40 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: WT
tissue: Thymus
age: P28 bc
individual: female #875
gender: female
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| Treatment protocol |
No Treatment was performed.
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| Growth protocol |
Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Thymic stromal cell isolation was done with slight modifications as described earlier (Rode et al., 2015). In contrast to the published method, minced thymi were directly subjected to digestion without discarding any fractions, and lymphoid cells (anti-CD45 beads, Miltenyi Biotec) and erythrocytes (anti-Ter119 beads, Miltenyi Biotec) were manually depleted using MACS technology.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
library of 96 WT TEC cells
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| Data processing |
For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Assembly: ENCODE VM9
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
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| Submission date |
Mar 29, 2022 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Sagar - |
| E-mail(s) |
sagar@uniklinik-freiburg.de
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| Organization name |
University Medical Center Freiburg
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| Department |
Department of Internal Medicine II
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| Lab |
Sagar
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| Street address |
Hugstetter Straße 55
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| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE106856 |
Developmental dynamics of two bipotent progenitors of thymic epithelium |
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| Relations |
| BioSample |
SAMN27063888 |
| SRA |
SRX14660249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5983101_T200_40.coutt.csv.gz |
315.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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