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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 19, 2018 |
| Title |
AB540 |
| Sample type |
SRA |
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| Source name |
Bone marrow hematopoietic progenitor single cells, Lin- cKit+
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
selection marker: Lin- cKit+
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| Treatment protocol |
For samples 122-133, 217-220 & samples 140-151, 221-222 mice were injected twice with 150 IU human erythropoietin (Recormon / Epoitin beta) or 4.8 µg human G-CSF (Neupogen) respectively and sacrificed on the third day
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| Growth protocol |
6 to 8 weeks-old mice housed at the Weizmann Institute animal facility
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Each mouse was euthanized and bone marrow harvested by crushing of the femur, tibia and ilia. Cell suspensions were stained with FACS antibodies and single cells sorted into capture plates (Jaitin et al, Science 2014)
Antibodies used: Lin = Ter119 (TER-119), CD11b (itgam), Gr-1 (RB8/8C5), CD3 (17A2), CD4 (GK1.5), CD8a (53-6.7), B220 (RA3/6B2); and cKit (2B8), Sca1 (D7), CD34 (RAM34), Flt3 (A2F10), FcgR (93), CD150 (TC15-12F12.2), CD24 (M1/69), CD11c (N418), I-A/I-E (M5/114), CD19 (1D3), NK1.1 (PK136), CD71 (R17217), SiglecH(551), CD22 (OX-97)
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample 34
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| Data processing |
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
metadata.txt (associates each single cell with its amplification batch and index sorting readouts)
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| Submission date |
Dec 19, 2016 |
| Last update date |
Jun 19, 2018 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
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| Phone |
972-8-9343338
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| Organization name |
Weizmann Institute of Science
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| Department |
Immunology
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| Street address |
234 Herzl st.
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| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE92575 |
Transcriptional plasticity, priming and commitment in hematopoietic lineages [RNA-seq] |
| GSE113495 |
Transcriptional plasticity, priming and commitment in hematopoietic lineages |
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| Relations |
| BioSample |
SAMN06164285 |
| SRA |
SRX2435743 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2432663_AB540.txt.gz |
445.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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