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| Status |
Public on Sep 06, 2016 |
| Title |
Lgr6+ rep1 |
| Sample type |
SRA |
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| Source name |
mammary gland
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| Organism |
Mus musculus |
| Characteristics |
cell type: Lgr6 positive
age: 5-week old
Sex: female
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary glands from Lgr6-eGFP-CreErt2 were dissected, mashed gently with a MACS dissociator (Miltenyi Biotec) and incubated in HBSS with 300U ml-1 collagenase (Sigma) plus 300 μg hyaluronidase (300U ml-1activity) (Sigma) and digested for 30m at 37°C. Red blood cells were lysed and samples digested with Trypsin for 3 min at 37°C before being filtered with a 70 by 40 μm-mesh. LIN- cells where then FACS sorted for LGR6+ cells.
RNA concentrations were determined with a Qubit fluorometer (ThermoFisher) as 7-25 pg/ul before analysis of RNA quality on a Bioanalyzer (Agilent) (RIN 5-8). cDNA (50-75ng/μl) was generated from 5μl RNA (NuGEN/Next-Gen), sheared (Covaris S-series), and cDNA fragments were cleaned-up (Zymo Research) before 10ng were used to generate an amplified cDNA library (NuGEN Ovation) over 18 PCR cycles. cDNA was sequenced on a HiSeq 4000 system (illumina) in paired-end 50 mode
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Lgr6_pos.R1
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| Data processing |
Gene level abundance estimates were generated using RSEM (v1.2.22) by mapping 50bp paired-end reads against the Mus musculus mm10 Refseq transcriptome and reference genome with the STAR (v2.4.2a) aligner.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene level raw abundance estimates for each sample.
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| Submission date |
Dec 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Axel Behrens |
| E-mail(s) |
axel.behrens@crick.ac.uk
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| Organization name |
Francis Crick Institute
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| Street address |
44 Lincoln's Inn Fields
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| City |
London |
| ZIP/Postal code |
WC2A 3LY |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE75648 |
RNA-Seq of Lgr6 positive and negative cells in mouse mammary gland |
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| Relations |
| BioSample |
SAMN04311919 |
| SRA |
SRX1460476 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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