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| Status |
Public on Dec 08, 2015 |
| Title |
Sox2 sample1 |
| Sample type |
SRA |
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| Source name |
sorted alveolar type 1 cells
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| Organism |
Mus musculus |
| Characteristics |
strain: mixed B6 and 129
age: P3-4
genotype: Scnn1a-Cre; Rosa[Sox2/+]
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| Extracted molecule |
total RNA |
| Extraction protocol |
Postnatal day 3 or 4 Scnn1a-Cre; RosamTmG/+ and Scnn1a-Cre; RosaSox2/+ littermate lungs were dissected in PBS. Around 3 mm wide strips were cut along the lobe edge, minced into pieces with forceps and digested in PBS with 2 mg/mL collagenase type I (Worthington,16 CLS-1) and 0.2 mg/mL DNase I (Worthington, D) for 40 min at 37 °C. An equal volume of 0.25% Trypsin/EDTA (Invitrogen, 25200-056) was added and incubated for another 10 min at 37 °C. Fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 5% and the tissue was triturated for 40~50 times. Dissociated cells were spun down at 6000 rpm for 1 min, resuspended in red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) for 3 min, washed with PBS with 1% FBS, SYTOX-red (Invitrogen, S34859) added to exclude dead cells and sorted on a BD Biosciences Influx sorter. RNA was extracted from at least 105 purified cells using Trizol reagents (Invitrogen, 15596018) and an RNeasy Micro kit (Qiagen, 74004).
100~200 ng total RNA was used to prepare an RNAseq library using an mRNA isolation kit (New England BioLabs, E7490) and a NEBNext Ultra RNA library prep kit (New England BioLabs, E7530S) with a final double (0.65 x -1 x bead volume) size selection step using a SPRIselect reagent kit (Beckman Coulter, B23318). Sequenced on an Illumina HiSeq2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls by standard Illumina pipeline.
35~80 million 76 nucleotide pair-end reads were generated for each sample and aligned to the UCSC mm10 reference genome using tophat2 and bowtie2.
Transcript abundance, differential expression, and isoform quantitation were calculated using the cufflinks and cuffdiff suite from each pair of littermate samples or pooled control and mutant samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
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| Submission date |
Oct 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Edwin Justin Ostrin |
| E-mail(s) |
ejostrin@mdanderson.org
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| Phone |
7137925389
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| Organization name |
MD Anderson Cancer Center
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| Department |
Pulmonary Medicine
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| Street address |
1515 Holcombe Blvd, Unit 1462
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE73861 |
Development and Plasticity of Alveolar Type 1 Cells |
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| Relations |
| BioSample |
SAMN04156841 |
| SRA |
SRX1318247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1904553_sample1.fpkm.txt.gz |
793.7 Kb |
(ftp)(http) |
TXT |
| GSM1904553_samples1and9vs2and10.fpkm.txt.gz |
966.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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