|
| Status |
Public on Jun 20, 2017 |
| Title |
hu_IPF_HTII280_5 |
| Sample type |
SRA |
| |
|
| Source name |
idiopathic pulmonary fibrosis patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung epithelial cells
facs purification: live, CD45-, Epcam+, HTII-280+
|
| Treatment protocol |
Tissue was mechanically and enzymatically disaggregated using dispase. Single cells were then stained with antibodies and flow sorted.
|
| Growth protocol |
n/a
|
| 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.
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 2500 |
| |
|
| Data processing |
bcl2fastq 1.8.4 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.
paired reads were aligned against hg19 using bowtie2-2.2.3 and tophat-2.0.13
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
|
| |
|
| Submission date |
Jun 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Vaughan |
| E-mail(s) |
[email protected]
|
| 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 |
GPL16791 |
| Series (2) |
| GSE83501 |
Human Single Cells - Local lung hypoxia determines epithelial fate decisions during alveolar regeneration |
| GSE83505 |
Local lung hypoxia determines epithelial fate decisions during alveolar regeneration |
|
| Relations |
| BioSample |
SAMN05267530 |
| SRA |
SRX1858397 |
