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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 19, 2024 |
| Title |
GVHD-081018-N3 |
| Sample type |
SRA |
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| Source name |
ileum
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| Organism |
Mus musculus |
| Characteristics |
tissue: ileum
cell type: CD45+H2kb+CD11b+Ly6G+
genotype: C57BL/6
treatment: allo-HCT with BM and T cells
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| Treatment protocol |
BALB/c recipient mice were irradiated with a lethal dose split into two single doses of 5 Gy each that were at least 4 h apart. The same day, recipients were injected intravenously with 5 x 10ˆ6 donor bone marrow cells and 4 x 10ˆ5 donor T cells (acute GVHD) or no T cells (control) from C57BL/6 mice.
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| Growth protocol |
C57BL/6N mice were bred in-house at the animal facility of the University Medical Center Freiburg or acquired from Janvier (France). Female mice between seven and ten weeks of age were used. BALB/c mice were acquired from Janvier (France) and used between seven and nine weeks of age.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Intestinal leukocytes were isolated by dissecting 4 cm intestinal segments and removal of Peyer’s patches. The segments were opened longitudinally and rinsed in PBS to remove the remaining feces. Epithelial cells were separated from the lamina propria using cell dissociation (CD) buffer (HBSS without Mg2+, Ca2+, 5 mM EDTA, 10 mM HEPES). The remaining tissue was digested with digestion buffer (HBSS with Mg2+, Ca2+, collagenase D 0.5 mg/ml, DNAse 0.5 mg/ml) to obtain single-cell suspensions.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016) and its modified version (Herman et al., 2018).
Adapted from TruSeq Small RNA Library Preparation Protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
aGVHD
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| Data processing |
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 09, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Nina Peltokangas |
| E-mail(s) |
peltokangas@ie-freiburg.mpg.de
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| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE227064 |
Lipocalin-2 expression identifies an immuno-regulatory intestinal neutrophil population during GVHD |
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| Relations |
| BioSample |
SAMN33706649 |
| SRA |
SRX19627183 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7090974_GVHD-081018-N3.coutt.csv.gz |
266.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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