|
| Status |
Public on Jun 11, 2015 |
| Title |
p2Cell_56_64 |
| Sample type |
SRA |
| |
|
| Source name |
whole e16.5 developing mouse lung, sacculation stage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: lung
age: e16.5 fetal mouse
genotype: wt
|
| Treatment protocol |
e16.5 pc pregnant females were euthanized via C02 and embryos were isolated and microdissected for developing lung buds; approximately 12 lung buds were combined to make a cell suspension to load into the Fluidigm C1
|
| Growth protocol |
Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microdissected mouse e16.5 lung buds were finely minced and triturated using a glass capillary pipette in protease serum free media, and suspended in approximately 100 uL of PBS and loaded into the Fluidigm C1 lab chip according to manufacturer protocol v1.x.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm9 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 148 cells
|
| |
|
| Submission date |
Jun 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan Xu |
| E-mail(s) |
[email protected]
|
| Organization name |
Cicinnati children's Hospital Medical Center
|
| Department |
Pulmonary Biology
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE69761 |
Fluidigm C1 + Illumina HiSeq quantitative whole transcriptome analysis of unsorted population of E16.5 lung cells |
|
| Relations |
| BioSample |
SAMN03769412 |
| SRA |
SRX1055958 |
