|
| Status |
Public on Nov 17, 2014 |
| Title |
CC10- B4+ single cells and K5-Cre+ single cells |
| Sample type |
SRA |
| |
|
| Source name |
distal lung epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: lung
age: 6-8 weeks
genotype: Scgb1a1tm1(cre/ERT)Blh / Gt(ROSA)26Sortm14(CAG-tdTomato)Hze
|
| Treatment protocol |
Mice were administered 3 doses of 0.25 mg / g body weight tamoxifen in 50 ul corn oil, with each dose seperated by 48 hours, and animals were housed 1 week prior to sacrifice. Lungs were exposed via standard procedures and perfused with PBS. After installation with agarose and subsequent hardening by a brief incubation on ice, each lobe was cut away from the mainstem bronchi. The proximal-most ¼ of each lobe surrounding the bronchi was then cut away to minimize the inclusion of basal cells in the cell preparation. Cells were incubated for 30 min at room temperature with anti-integrin B4, anti-EpCam-PE, and sytox blue, washed, and sorted.
|
| 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 |
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions. As a bulk control, cDNA was prepared from approximately 200 cells in a PCR tube using the same protocol and reagents as used for the single cells. In addition, one "no cell control" was prepared using reagents without any cell input in a PCR tube.
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 NextSeq 500 |
| |
|
| Description |
all are processed FPKM files
|
| 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 mm10 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Sep 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Vaughan |
| E-mail(s) |
andrewva@vet.upenn.ed
|
| Phone |
2062939309
|
| Organization name |
University of Pennsylvania
|
| Street address |
3800 Spruce Street
|
| City |
PHILADELPHIA |
| State/province |
United States |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE61300 |
High throughput quantitative whole transcriptome analysis of CC10- B4+ and Krt5-CreERT2 - labeled distal lung cells |
|
| Relations |
| BioSample |
SAMN03031651 |
| SRA |
SRX699017 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1501785_exp1_c01.fpkm_tracking.gz |
598.6 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c16.fpkm_tracking.gz |
623.3 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c20.fpkm_tracking.gz |
591.7 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c22.fpkm_tracking.gz |
593.8 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c25.fpkm_tracking.gz |
597.3 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c28.fpkm_tracking.gz |
601.8 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c30.fpkm_tracking.gz |
588.3 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c35.fpkm_tracking.gz |
608.3 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c37.fpkm_tracking.gz |
596.5 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c38.fpkm_tracking.gz |
616.3 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c39.fpkm_tracking.gz |
621.5 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c44.fpkm_tracking.gz |
608.9 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c50.fpkm_tracking.gz |
627.1 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c52.fpkm_tracking.gz |
591.6 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c53.fpkm_tracking.gz |
606.6 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c60.fpkm_tracking.gz |
602.6 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c69.fpkm_tracking.gz |
610.4 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c72.fpkm_tracking.gz |
623.1 Kb |
(ftp)(http) |
FPKM_TRACKING |
| GSM1501785_exp1_c78.fpkm_tracking.gz |
600.2 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
